Sample Manager User Guide Agilent Genomic Workbench 5.0
Sample Manager Agilent Genomic Workbench 5.0 User Guide Agilent Technologies Notices © Agilent Technologies, Inc. 2009 Warranty No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or translation into a foreign language) without prior agreement and written consent from Agilent Technologies, Inc. as governed by United States and international copyright laws. The material contained in this document is provided “as is,” and is subject to being changed, without notice, in future editions. Further, to the maximum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a particular purpose. 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It calls attention to an operating procedure, practice, or the like that, if not correctly performed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met. Sample Manager User Guide In This Guide... This guide describes how to use the Sample Manager tab of Genomic Workbench to organize microarrays and edit their attributes. 1 Setting Up Sample Manager This chapter describes how to organize microarrays and edit their attributes. 2 Sample Manager Reference This chapter describes the Sample Manager main window and dialog boxes. Sample Manager User Guide 3 4 Sample Manager User Guide Contents 1 Setting Up Sample Manager 7 To open Sample Manager 9 To import an Attribute File 9 To add an Array ID to an existing data folder 10 To add a new data folder 10 To remove an Array ID 11 To remove a data folder 11 To add, change, or remove attributes 11 To edit the attribute values of a specific microarray To export attributes 13 To show or hide attributes 14 2 Sample Manager Reference 15 Main Window Reference 16 Sample Manager Command Ribbon Data Navigator 18 Sample Utility Tab 20 17 Dialog Box Reference 22 Add Array ID to Data Folder 22 Attribute File Importer-Map Column Headers Attributes 26 Export 29 Export Attribute Files 30 Import Attribute Files 33 Input Attribute Name 34 Show/Hide Columns 35 Sample Manager User Guide 13 23 5 Contents 6 Sample Manager User Guide Agilent Genomic Workbench 5.0 – Sample Manager User Guide 1 Setting Up Sample Manager To open Sample Manager 9 To import an Attribute File 9 To add an Array ID to an existing data folder 10 To add a new data folder 10 To remove an Array ID 11 To remove a data folder 11 To add, change, or remove attributes 11 To edit the attribute values of a specific microarray 13 To export attributes 13 To show or hide attributes 14 This section provides how- to help for the tasks available in the Sample Manager tab of Agilent Genomic Workbench. For a description of each part of this tab, including all of the dialog boxes that can appear when you click buttons and other elements, see “Main Window Reference” on page 16, and “Dialog Box Reference” on page 22. About Sample Manager When you scan a hybridized microarray slide, the Agilent Scanner produces a *.tif image file that includes the identifying barcode from the slide. This barcode, embedded in the header of the *.tif file, uniquely identifies the slide. A microarray slide can contain one array, or for multi- pack arrays, multiple arrays on the same slide. The scanned data from each array corresponds to a particular sample, and each array on a slide has a unique Array ID; thus, each sample is associated with a specific Array ID. The attributes that are assigned for each Array ID are carried with the Array ID for the rest of the analysis on Genomic Workbench. Agilent Technologies 7 1 Setting Up Sample Manager In Sample Manager, you can define and edit the attributes associated with each microarray, such as biological sample used, the amount of label used, or the hybridization date. You can export attributes to an Attribute File. Later, you can import the file into Genomic Workbench to load or restore the saved attributes. Attribute files can contain attributes for one or more microarrays. After you organize your microarrays and define their attributes, you can use the Workflow feature of Genomic Workbench to automatically run Feature Extraction and convert the scanned images of your arrays into log ratio data that you can analyze with other parts of Genomic Workbench. Note that the capabilities you have will depend on the software and licenses you have installed. The attributes that are assigned for each Array ID are carried with the Array ID for the rest of the analysis on Genomic Workbench. About Attribute Files An Attribute File contains identification information (Array ID and Barcode) and attributes for one or more microarray samples. Sample attributes may vary, but at a minimum a set of information in an attribute file for a 2 color microarray experiment must include Array ID, Red Sample ID, Green Sample ID, and Polarity values. For a 1- color experiment, the user needs to provide the Array ID and Green Sample ID. Attribute files are often created by the user with a spreadsheet program and should be saved as a tab- delimited text file or .xls file. For details on how to open an attribute file, see “To import an Attribute File” on page 9. 8 Sample Manager User Guide Setting Up Sample Manager 1 To open Sample Manager Sample Manager is used to organize microarrays and to define and edit their attributes. 1 Start Genomic Workbench. 2 On the Genomic Workbench tab menu, click Sample Manager. Or, click Sample Manager from the Open Application tab. The main window for Sample Manager appears. See “Main Window Reference” on page 16 for details. To import an Attribute File When you import an attribute file the information in the file will be displayed in rows in the Sample Utility tab. For details on Attribute Files, see “About Attribute Files” on page 8. NOTE Attribute Files must be either tab-delimited .txt files or .xls files, and cannot be formulas (only simple text). If you want to import an .xlsx spreadsheet file, you must first save it as an .xls file (Excel 97-2003 Workbook format). 1 From the Sample Manager Command Ribbon, click Import Attribute File... 2 Browse to the location where your attribute file is located, click on it to select it, and then click Open. The Import Attribute Files dialog box opens. 3 Browse to a folder location and click to select a file, or type the name of the file to be imported. Click Open. The Attribute File Importer - Map Column Headers dialog box opens. 4 Complete the information for the attribute file to be imported. See “Attribute File Importer- Map Column Headers” on page 23 for an explanation of the available options and commands. 5 Click Import. The data in the file will be imported and displayed in the Sample Utility spreadsheet. Sample Manager User Guide 9 1 Setting Up Sample Manager NOTE Attribute Files contain only Array IDs and the associated sample attributes. They do not contain feature data from the scanned images of microarrays. To add an Array ID to an existing data folder You can add a row to a displayed data folder. 1 Click Add Array ID. The Add Array ID to Data Folder dialog box appears. See “Add Array ID to Data Folder” on page 22. 2 Select the node to which you want to add an array ID row. 3 Click OK. 4 A row is added to the array list. In the blank fields, enter the attributes for the microarray and then click Save Changes. To add a new data folder You can manually add a new data folder to the Array Data folder. 1 Click Add Array ID. The Add Array ID to Data Folder dialog box appears. See “Add Array ID to Data Folder” on page 22. 2 Type a name for the new data folder. 3 Click OK. 4 A row is added to the array list. In the blank fields, enter the attributes for the microarray and then click Save Changes. The new data folder appears in the Array Data list in the data navigator pane. 10 Sample Manager User Guide Setting Up Sample Manager 1 To remove an Array ID You can remove one or more rows from a displayed data folder. 1 In the Sample Utility tab, click to select an Array ID. To select a series of Array IDs, hold the SHIFT key and then click the first and then the last Array ID to be removed. 2 Click Remove Array ID(s). The selected row(s) will be removed from the spreadsheet. 3 Click Save Changes to save the array list with the changes. To remove a data folder You can remove an array data folder that contains Array IDs that have been imported from an attribute file or created in Sample Manager. To remove a data folder, 1 In the Data Navigator, do a right- click on the data folder you wish to delete. 2 Select Delete. The selected data folder will be deleted from the Sample Manager. NOTE Array data from imported FE or UDF files cannot be deleted from Sample Manager. They must be deleted from one of the interactive tabs. See “To remove data or design files from the program” on page 33 of the Data Viewing Guide for details. To add, change, or remove attributes Sample attributes are pieces of microarray- specific information, such as hybridization temperature or sample name. Genomic Workbench maintains a standard set of attributes that you can define for individual microarrays. You can add new attributes to this set and delete existing ones. You can also edit existing attributes. For information about how to define attributes for a specific microarray, see “To edit the attribute values of a specific microarray” on page 13. Sample Manager User Guide 11 1 Setting Up Sample Manager To add a microarray attribute 1 Click Add/Edit Attribute. The Attributes dialog box appears. See “Attributes” on page 26. 2 At the bottom of the dialog box, click New (not New Value). The Input dialog box appears. 3 Type a name for the attribute of up to 50 characters in length, and then click OK. The new name appears in the Attributes dialog box. 4 Edit the details of the new attribute. See “Attributes” on page 26 for an explanation of the available options and commands. 5 Click Update. 6 Click Close. You can now define the new attribute for any sample in the program. To change an existing attribute 1 Click Add/Edit Attribute. The Attributes dialog box appears. 2 Click the Name arrow and select the attribute you want to edit. 3 Edit the details of the attribute. For details about editing options, see “Attributes” on page 26. 4 Click Update. 5 Click Close. To delete a attribute 1 Click Add/Edit Attribute. The Attributes dialog box appears. 2 Click the Name arrow and select the attribute you want to delete. 3 Click Delete (Not Delete Value). 4 You will be asked to confirm that you want to delete the attribute. Click Yes to permanently delete the attribute. Click No to abort the delete process and return to the Attributes dialog box. 5 Click Close. 12 Sample Manager User Guide Setting Up Sample Manager CAUTION 1 Deleting an attribute permanently removes the attribute and its associated values from Genomic Workbench. To restore the attribute, you must create it again from scratch. To edit the attribute values of a specific microarray You can define or change the values of attributes assigned to a specific microarray. 1 In the Sample Utility tab, click on a microarray to select it. 2 Double- click the sample attribute you wish to change for this microarray. The attribute box will become active. 3 Type the new attribute value or click the arrow to select the new value from a list. 4 When finished, click Save Changes. NOTE Save Changes does not update the attribute file on the hard disk. In order to save the changes in the attribute file, you must export the attribute file. See “To export attributes” on page 13. To change the value of an attribute globally (to apply to all samples with that attribute) use the Add/Edit Attribute function. See “Attributes” on page 26. To export attributes After you organize microarrays and define their attributes, you can save one or more of them in an Attribute File. (See “To edit the attribute values of a specific microarray” on page 13.) Later, you can re- import this attribute file into Genomic Workbench to recreate or restore attributes. 1 Click Export Attribute File... The Export Attribute Files dialog box appears. See “Export Attribute Files” on page 30. 2 In the Array tab, select the Attribute File containing the microarrays you want to export. Sample Manager User Guide 13 1 Setting Up Sample Manager 3 In the Array list select the sample arrays you want to export. Click one or more of the arrow buttons to move them to the Selected Array List. 4 Click Next. The Attribute tab is displayed. 5 Select the Attributes you want to export and then click OK. The Export dialog box opens. See “Attributes” on page 26 6 In the Export dialog box, browse to the location where you want to save the exported attribute file, type a name for the file, and then click Export to save it. To show or hide attributes You can customize the attributes columns that are displayed in the Sample Utility tab. 1 In the Sample Utility tab, click Show/Hide Attributes. The Show Columns dialog box appears. Columns that show by default are grayed- out. See “Show/Hide Columns” on page 35 for details. 2 Click to select the blue boxes next to each columns you wish to display in the Sample Utility tab. Click again to de- select a box. 3 When all desired attributes are selected, click Save to update the Sample Utility spreadsheet. 4 Click Close to close the Show/Hide Columns dialog box. 14 Sample Manager User Guide Agilent Genomic Workbench 5.0 – Sample Manager User Guide 2 Sample Manager Reference Main Window Reference 16 Dialog Box Reference 22 This chapter describes the Genomic Workbench Sample Manager main window and dialog boxes. Agilent Technologies 15 2 Sample Manager Reference Main Window Reference This section contains descriptions of each element of the Sample Manager tab. The main window opens when you click the tab in Genomic Workbench, The window contains elements identified and described in Figure 1 and Table 1. Tab Menu Command Ribbon Search Pane Sample Utility Tab Data Navigator Utility Buttons Figure 1 16 Sample Manager – Main Window Sample Manager User Guide Sample Manager Reference Table 1 2 Sample Manager – Main Window Elements Part Purpose Tab menu Click tabs to switch from one functional area of Genomic Workbench to another. Command Ribbon Contains the commands used to perform Sample Manager functions, such as import and export Attribute Files. Data Navigator Displays list of microarrays, organized into folders representing imported files. Search Pane Used to locate an array ID in the list. Type the array ID to search for and then click the search button to find and highlight that array in the list. Sample Utility tab Contains a list of all available sample microarrays, organized by Array ID. Attributes displayed can be selected by the user, but at a minimum Array ID, Green Sample, Red Sample, Polarity, and Extraction Status are displayed. Utility Buttons Buttons used to edit and add to the sample microarray list, and for saving or canceling changes. Sample Manager Command Ribbon Figure 2 Sample Manager Command Ribbon The Sample Manager Command Ribbon contains the commands used for importing and exporting attribute files. Sample Manager User Guide 17 2 Sample Manager Reference Table 2 Sample Manager Ribbon Select Purpose Import Attribute File... To import contents of an Attribute File. Export Attribute File... To export the current Sample Utility data to an Attribute File. Data Navigator Figure 3 18 Sample Manager Data Navigator Sample Manager User Guide Sample Manager Reference 2 The Data Navigator for Sample Manager contains an Array Data folder, which contains one or more Data folders. Each of these folders contains a list of microarrays for which attributes exist in the program. You can use the Data Navigator to: • view the microarrays for each imported data file • delete a single microarray • delete an entire set of microaray attributes (Data folder) • search for a single Array ID Table 3 Icon Data Navigator icons, special text, and buttons Comments Click to expand a folder and display its contents. Click to collapse a folder and hide its contents. A folder that contains data. In the case of Array Data, each folder, or “Data folder” contains a list of the microarrays in that imported attribute file. If you are using one of the Genomic Workbench licensed applications, a folder may contain Experiment, Design, or any type of imported file. Arrays that were imported using one of the interactive tabs are not editable and will appear “grayed out” in the Sample Utility list. A single microarray. The Detach button, located at the top of the Data Navigator pane, detaches the Data Navigator pane from the main window, and opens it in its own new window. Click to detach only the Array Data panel. Click again to re-attach the panel to the Data Navigator. Click to find an Array ID entered in the Search box. Data Navigator actions and shortcut menus Within the Data Navigator, you can perform the following shortcuts and actions. • Double- click a Data folder to expand or collapse it. Sample Manager User Guide 19 2 Sample Manager Reference • Double- click a Data folder to view all arrays along with their attributes in the Sample Utility data view tab. • Double- click an individual array to highlight that array in the Sample Utility data view tab. • Double- click the name of a folder (or design or application type if using licensed software) to view a list of its associated samples and their attributes in the Sample Utility data view tab. Sample Utility Tab Figure 4 20 Sample Manager – Sample Utility Tab Sample Manager User Guide Sample Manager Reference 2 The Sample Utility tab displays the list of microarrays that are currently selected in the Data Navigator. See “Data Navigator actions and shortcut menus” on page 19. Each microarray is displayed along with its sample attributes and its Extraction Status. Buttons at the bottom of the tab are used to display or edit sample attributes and perform other tasks on the list, as described in the table below. See “Dialog Box Reference” beginning on page 22 for details on these buttons and their use. NOTE Attributes for microarrays that have been extracted are not editable, and appear “grayed out”. Table 4 Sample Utility Tab Buttons Button Function Show/Hide Attributes Opens Show/Hide columns dialog box where user can select which attributes to display. See “Show/Hide Columns” on page 35. Add/Edit Attribute Opens Attributes dialog box where user can add a new attribute or edit an existing attribute. “Attributes” on page 26. Add Array ID Used to add a single Array ID to a folder. See “Add Array ID to Data Folder” on page 22. Remove Array ID Removes selected Array ID from the list. Save Changes Saves changes made to the array list. Cancel Changes Cancels changes made to the array list. Sample Manager User Guide 21 2 Sample Manager Reference Dialog Box Reference Add Array ID to Data Folder Figure 5 Add Array ID to Data Folder dialog box Purpose: Adds an Array ID row to the list in the Sample Utility tab. Also used to add a new Array folder to the Array Data. To open: This dialog box appears when you click the Add Array ID button at the bottom of the Sample Utilities pane. Select Node OK Cancel NOTE 22 Click the arrow and select one of the current data folders, or type the name of a new data folder. Click OK to add a blank array row to the selected data folder, or to create the new data folder and add an Array ID row to it. Click Cancel to cancel the operation without adding an array ID. When using the Add Array ID function to add a data folder, you must enter the required attributes for the new array and then Save Changes in order for it to appear in the Array Data list. Sample Manager User Guide Sample Manager Reference 2 Attribute File Importer-Map Column Headers Figure 6 Attribute File Importer - Map Column Headers dialog box Purpose: Use this dialog box to map column headers from an attribute file created using a spreadsheet program to the headers expected by the Sample Manager program (if necessary) and to import the file. To open: This dialog box opens when you click Open in the Import Attribute Files dialog box. To map a column header 1 Click the arrow and select the attribute header to be mapped from the list of currently- defined attributes. 2 When all columns are mapped, click Import to import the file. Attribute File Properties Channel Properties Select the number of lines to be skipped for the header row in the imported file. Click the arrow to change the number of channels for the file. For a 1- color experiment, select 1. For a 2- color experiment, select 2. Sample Manager User Guide 23 2 Sample Manager Reference Reset Resets the current mapping changes to the defaults when the file was opened. Import Imports the file. For a list of exceptions and conditions for importing files, see Table 6 on page 25. Cancel Cancels the file import operation and closes the dialog box. Table 5 Mandatory Columns in an Attribute File Column Requirements For one-channel arrays Array ID Unique for each sample Green Sample Green sample ID. For two-channel arrays Array ID Unique for each sample Green Sample Green Sample ID. Red Sample Red Sample ID. Polarity Value of 1 or -1 only. Blank value will be set to “1”. Values other than 1, -1 or blank will cause the row to be skipped and not imported. If a polarity is assigned as -1, then for later analysis using Genomic Workbench, it is treated as a dye-flip array. Dye-flip arrays are described in “To import Agilent FE or GenePix/Axon data files” on page 13 in the Data Viewing User Guide. 24 Sample Manager User Guide Sample Manager Reference Table 6 Exceptions and Conditions for Importing Attribute Files Condition Outcome The attribute file being imported has more than 1 entry for the same Array ID. Error message appears. User is asked whether the last entry should overwrite the previous entry. The attribute file to be imported has rows with missing mandatory column values. The row will be skipped and an error message will appear containing information on the missing mandatory column value(s). The attribute file to be imported has rows with values that do not match the data type for the particular column. Those rows will be skipped and a message will be presented warning the user. The attribute file to be imported has rows with Array IDs already present in the table. Error message appears “Some Array ID’s are already present Do you want to over-write these rows? Click Yes to over-write the existing rows with the duplicate rows from the attribute file. Click No to cancel the import. The attribute file to be imported has rows with ArrayID already present in the table as FE data (gray row). Polarity and isMultiPack value will not be overwritten. Sample Manager User Guide 2 25 2 Sample Manager Reference Attributes Figure 7 Attributes dialog box Purpose: You use this dialog box to create, change, or delete sample attributes for the arrays displayed. Attributes are pieces of sample- specific information, such as hybridization temperature or sample name. To open: The Attributes dialog box opens when you click Add/Edit Attribute from the Sample Utilities view. NOTE Name Attributes added or edited in this dialog box will apply to all array samples containing the attribute. To assign values to attributes for individual samples, see “To edit the attribute values of a specific microarray” on page 13. The name of the attribute whose details appear in the dialog box. Click the arrow to select the desired attribute from the list. Two lists appear to the right of the attribute name. These lists define the type of value the program expects for the attribute. You select one value from each list. 26 Sample Manager User Guide Sample Manager Reference 2 The Type list offers these options: Option The attribute is: int an integer double a double-precision floating point number (a high-precision number that can include decimals) boolean true or false text a string of plain text The Property list offers these options: Value New Value Delete Value Option Description Extendible List When this is selected, the user can define a choice of defined values that will be displayed when the user selects this attribute box. It also displays a text box for a custom value. Single valued The program displays a single text box when you edit this attribute for a specific sample. Dynamic valued The program does not allow you to edit the value of this attribute for a specific sample. Instead, it defines the value of the attribute based on information in the array data file. Pre-defined list When you edit the attribute for a specific sample, the program offers choices for the value of the attribute. The program offers these values as choices when you edit the selected attribute for a specific sample. Values only appear in this list for multi- valued attributes. Double- click a value to change it. Press Update to accept the edited value. Press Reset to return the values to their previous state. Adds another value to the Value list. This command is only available for multi- valued attributes. Double- click the new (blank) value to make it available for editing. Press Update to accept the edited value. Deletes a value from the Value list. This command is only available for multi- valued attributes. Click the value you want to delete, then click Delete Value. Sample Manager User Guide 27 2 Sample Manager Reference New Update Reset Delete CAUTION Close 28 Use this command to create a new attribute. It opens an Input dialog box, where you can type a name for the new attribute. See “Input Attribute Name” on page 34. (Enabled only if there are unsaved changes to the attribute.) Saves the changes you made to the attribute without closing the Attributes dialog box. (Enabled only if there are unsaved changes to the attribute.) Restores the attribute it to its state before you made any changes. Deletes the attribute from the program. If you delete an attribute, the program also deletes all values assigned to it for all samples. To restore the attribute, you must create the attribute again, and re-assign the desired value to each array. Closes the Attributes dialog box. If you made changes to the attribute, but did not save them, a dialog box asks if you want to save the changes to the attribute. Click Yes to save the changes, or click No to close the dialog box without saving the changes, or click Cancel to go back to the Attributes dialog box without saving the changes. Sample Manager User Guide Sample Manager Reference 2 Export Figure 8 Export dialog box Purpose: Used to designate a file name and location for exporting data to an Attribute File. To open: The Export dialog box opens when you click Export from the Export Array Attributes - Attributes tab. Look in File name Files of type Use the arrow to select the folder location for saving the attribute file. If necessary, use the adjacent buttons to move up one folder, look in the desktop, or create a new folder. You can also change the file view to include a list or details. Type the name to be used for the attribute file. Click the arrow to change the file types displayed. Export Saves the designated microarray attributes in the designated file. A message appears to inform you that the file was exported successfully. Cancel Closes the Export Attribute Files dialog box without exporting an Attribute File. Sample Manager User Guide 29 2 Sample Manager Reference Export Attribute Files Purpose: This dialog box contains two tabs used to define what data are to be exported to the exported attribute file. To open: This dialog box opens when you click Export Array Attributes... on the Sample Manager Command Ribbon. Export Attribute Files - Array tab Figure 9 Export Attribute Files dialog box - Array Tab Purpose: This tab is used to select the arrays you wish to export. Once you have selected the arrays you wish to export, click Next. This will open the Export Attribute Files - Attribute tab. To open: From the Command Ribbon, click Export Attribute Files... and then click the Array tab. Attribute Files 30 Select an attribute file from the list. The sample arrays from this attribute file will be displayed in the Arrays list. After you have selected arrays for export from this file, you can select another attribute file from which arrays can be selected. In this way you can create a custom attribute file that contains some or all of the arrays from any open attribute file. Sample Manager User Guide Sample Manager Reference Array list 2 Displays a list of available arrays for export. Move desired arrays for export to the Selected Array List using one of the following methods. • To select an array for subsequent transfer to the Selected Array List, click its name. • To select additional arrays, control- click their names. • To select a contiguous block of arrays, click the name of the first array, then shift- click the name of the last one. Selected Array List Displays the arrays currently selected for export. Moves the selected arrays in Array List to the Selected Arrays List. Moves all of the arrays in Array List to the Selected Arrays List. Removes an array from the Selected Array List. To select an array for removal, click its name. If desired, you can re- add an array. Clears the Selected Array List. Next Cancel Moves to Attribute tab for selection of attributes. See “Export Attribute Files - Attribute Tab” on page 32. Closes the dialog box without selecting any array attributes to be exported. Sample Manager User Guide 31 2 Sample Manager Reference Export Attribute Files - Attribute Tab Figure 10 Export Attribute Files dialog box - Attribute Tab Purpose: This tab is used to select the attributes you want to include with the exported array samples. When you have finished selecting the attributes to be exported, click OK and the Export dialog box will appear where you can designate the file name. See “Export” on page 29. To open: From the Command Ribbon, click Export Attribute Files... and then click the Attribute tab, or click Next> after selecting Arrays. Attribute list Displays a list of available attributes for export. Move desired attributes for export to the Selected Attribute List using one of the following methods. • To select an array for subsequent transfer to the Selected Attributes List, click its name. • To select additional attributes, control- click their names. • To select a contiguous block of attributes, click the name of the first attribute, then shift- click the name of the last one. Selected Attribute List 32 Displays the attributes currently selected for export. Sample Manager User Guide Sample Manager Reference 2 Moves the selected attributes in the Attribute List to the Selected Attributes List. Moves all of the arrays in Array List to the Selected Arrays List. Removes an attribute from the Selected Array List. To select an array for removal, click its name. If desired, you can re- add an array. Clears the Selected Array List. Back Cancel Moves to Array tab for selection of arrays. See “Export Attribute Files Array tab” on page 30. Closes the dialog box without selecting any array attributes to be exported. Import Attribute Files Figure 11 Import Attribute Files dialog box Purpose: You use this dialog box to load an attribute file into the program. Sample Manager User Guide 33 2 Sample Manager Reference To open: The Import Attribute Files dialog box opens when you click Import Attribute Files... from the Sample Manager Command Ribbon. Look in File name Type the attribute file name or click to select it from the list of files. Files of type Click the arrow to change the file types displayed. Open Cancel Use the arrow to select the folder location where the attribute file is located. If necessary, use the adjacent buttons to move up one folder or look on the desktop. You can also change the file view to include a list or details. Once you have designated a file name and location, click this to open the Attribute File Importer dialog box. See “Attribute File Importer- Map Column Headers” on page 23. Closes the dialog box without importing anything. Input Attribute Name Figure 12 Input dialog box Purpose: To enter the name of a new attribute you are creating. To Open: Click Add/Edit Attribute. From the Attributes dialog box, click New. Enter name for new attribute OK Cancel 34 Type the name for the attribute you wish to add. Click OK to accept the new attribute name. Click this to cancel the new attribute. Sample Manager User Guide Sample Manager Reference 2 Show/Hide Columns Figure 13 Show/Hide Columns dialog box Purpose: Used to select the attributes that will be displayed in the Sample Utilities tab. To open: This dialog box appears when you press the Show/Hide Attributes button at the bottom of the Sample Utilities tab. All available attributes are shown in the Attributes column. Attributes with a check- mark next to them will be displayed in the Sample Utilities tab for each sample. To select an attribute for display, click the Show in Table box next to it. To de- select a currently- selected attribute, click the Show in Table box again. Save Select All Deselect All Close Saves the current list of selected attributes and updates the Sample Utilities table based on the selections. Selects all the attributes in the list. Removes all check marks from attributes in the list. Closes the dialog box. If changes have been made, the program asks if you want to save your changes before closing. Sample Manager User Guide 35 2 36 Sample Manager Reference Sample Manager User Guide www.agilent.com In This Book This guide describes how to use the Sample Manager tab of Genomic Workbench to organize microarrays and edit their attributes. Agilent Technologies, Inc. 2009 First Edition, April 2009 Agilent Technologies
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