PGS Documentation

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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. 

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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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