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Associating a Spreadsheet with an Annotation File

For Partek^® Genomics Suite^® to recognize an annotation spreadsheet, it must meet several requirements. First, there must be a column header row in the annotation file. Second, there must be a column in the annotation file that matches the identifiers in your data spreadsheet. Third, any text field above the column header row must start with #. Fourth, the text fields must be tab or comma delimited. 

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• Verify that a column in the annotation file matches the identifier in your data spreadsheet, e.g probe ID, the identifier must be unique to each row
• Remove the text before the first column header (Figure 1) or add # to each text box 
• Save the annotation file as a .txt file

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Depending on how you imported the data, you may see a Configure Spreadsheet dialog (Figure 3). Select the most appropriate option for your data; here we have chosen Genomic microarray. 

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An index file for the genomic location data of the annotation file is generated in the same folder as the annotation file; it has the same file name as the annotation file, but the file extension .idx. If you need to re-configure the genomic location field in the annotation file, first manually delete the .idx file and re-do the above steps to generate a new index file for the annotation file.

The Chip/Reference text field will be populated with the annotation file name. You can edit this text field this if you wish. 

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The Column Configuration section of the Add Rows/Columns to Spreadsheet dialog should contain all the feature annotations from the annotation file spreadsheet (Figure 6). Here we selected ILMN_Gene, which will add gene name information as a column next to 1. ID_REF. 

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