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If it is difficult to visualize where the column headers start, it might help to import the annotation file into a spreadsheet viewing program such as Microsoft Excel or Google Sheets. 

 

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SubtitleTextThe HumanHT-12 v4.0 Gene Expression BeadChip annotation file contains several rows of information prior to the column header row. To use this annotation file in Partek Genomics Suite, we delete any rows prior to the column headers row.
AnchorNameModifying Annotation File

  • Right click the spreadsheet you want to annotate in the spreadsheet tree panel
  • Select Properties from the pop-up menu (Figure 2)

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SubtitleTextChanging the spreadsheet properties
AnchorNameChanging spreadsheet properties

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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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  • Select Close to return to the Configure Genomic Properties

 


 

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SubtitleTextSpecifying the columns that contain the genomic locations of markers in the annotation file
AnchorNameConfiguring Annotation

 

 

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

  • Select the species and genome from the Species and Genome Build section of the dialog; we have chosen Homo sapiens and hg19 (Figure 4)

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SubtitleTextChoosing annotation file using the Configure Genomic Properties dialog
AnchorNameChoosing Annotation File

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  • Select OK apply the annotation file to your data spreadsheet

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  • Right-click on a column in the annotated data file spreadsheet
  • Select Insert Annotation from the pop-up menu (Figure 5)

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SubtitleTextAdding an annotation column to data spreadsheet
AnchorNameAdding an annotation column

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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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SubtitleTextAnnotations from the annotation spreadsheet file should appear as options in the Column Configuration section of the Add Rows/Columns to Spreadsheet
AnchorNameAdd Rows/Columns to Spreadsheet

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Annotation features can also be added to the Genome Viewer as tracks. See (chapter on genome viewer) for an introduction to adding tracks. 

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