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The preferred method for importing a generic data spreadsheet into Partek ^® Genomics Suite ^® is as a text file. Here, we illustrate importing a list of genes with p-value and fold-change from an experiment comparing two conditions. 

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The File Type section of the Import dialog includes a preview of the text file and import options (Figure 1). 

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The next step is to identify where the data starts and where the optional header is found using Identify Column Labels, Start of Data (Figure 3). The line that contains the header (if present) must precede the data. If there are lines to be skipped in the file (like comments), they may only appear at the top of the file, before the header line or data begin.

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If there are missing numerical values or empty cells in your input list, insert a special character or symbol (?, N/A, NA, etc.) in the missing cells; you will specify the character in the Missing Data Representation section of the dialog, only one symbol can be used to represent missing values, the default missing value indicator is ?. 

• If a header row is present, select Col Lbls to allow you to select a column header row
• Select the row where the data beings using the Begin Data selector 
• If any cells have a missing value, you can signify this with a special symbol selected using the Missing Data Representation panel

Signifying missing data is important if you have empty cells in a column that you plan to use for statistical analysis because missing values can cause statistical tests to fail. The default missing value indicator is ?. 

• Select Next > 

The Preview text encoding section (Figure 4) previews the first five lines of the file, allowing you to check if the text encoding is correct. 

• If the text does not appear properly, use the Specify the text encoding: drop-down menu to choose the correct encoding 

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The final section of the Import .txt, .tsv, or .csv File dialog is Verify Type & Attribute of Data Columns (Figure 5). While data column type and attribute can be modified after import, it is easier and faster to select the proper options during import as multiple columns may be selected during this dialog.  

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If there is an identifier like gene symbol or SNP, the Type field for that column should be set to text and Attribute should be set to label. Numeric values (intensities, p-values, fold-changes, etc.) should have Type set to double and Attribute set to response. The other possible value for Attribute is factor and describes sample data. The user interface is this dialog allows you to select multiple columns at once (Ctrl+left click and Shift+left click). The interface controls are detailed in the dialog (Figure 5). 

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If Genomic data was selected in the Data Type section, the Configure Genomic Properties dialog will open (Figure 6). These options will be discussed in the next section when we add an annotation file.  

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• Select OK 

The imported spreadsheet will open (Figure 7). 

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