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The subject factor in the ANOVA model is listed as “8. Subject (6. Type)” this means that Subject is nested in Type. PGS Partek Genomics Suite can automatically detect this sort of hierarchical design and will adjust the ANOVA calculation accordingly.
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Now that you have obtained statistical results from the microarray experiment, you can now take the result of 22,283 genes and create a new spreadsheet of just those genes that pass certain criteria. This will streamline data management by focusing on just those genes with the most significant differential expression or substantial fold change. In PGS, the The List Manager can be used to specify numerous conditions to use in the generation of our list of genes of interest. In this tutorial, we are going to create a gene list with a fold change between -1.3 to 1.3 with an unadjusted p-value of < 0.0005.
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You should take some time creating new gene list criteria of your own to become familiar with the List Manager tool in PGS. For more information, you can always click on the (
) buttons.
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- Select the 1/ANOVA-3way (ANOVAResults) spreadsheet in the Analysis tab. Thisis the spreadsheet we will be using to create the gene list
- Select View > Volcano Plot from the PGS Partek Genomics Suite main menu (Figure 10)
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- Select Rendering Properties (
) - Choose the Axes tab
- Check Select all points in a section to allow PGS Partek Genomics Suite to automatically select all the points in any given section
- Select the Set Cutoff Lines button and configure the Set Cutoff Lines dialog as shown (Figure 12)
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