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The result will be displayed in a child spreadsheet, ANOVA-3way (ANOVAResults). In this spreadsheet, each row represents a gene and the columns represent the computation results for that gene (Figure 4). By default, the genes are sorted in ascending order by the p-value of the first categorical factor. In this tutorial,Type is the first categorical factor, which means the most highly significant differently expressed gene between Down syndrome and normal samples is at the top of the spreadsheet in row 1.
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You basically identify genes with probesets. Although this is convenient and straightforward, it is not actually true. Perhaps a sentence explaining that for convenience these terms will be treated as synonims, although... |
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We can view the expression levels of a gene for each sample using a dot plot.
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Please explain the error bars on the interaction plot |
- Right click on the gene row header and select Dot Plot (Orig. Data) from the pop-up menu. This generates a Dot Plot tab for the selected gene (Figure 8)
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- Set X Axis (Fold-Change) to 12. Fold-Change(Down Syndrome vs. Normal), and the Y axis (p-value) to be 11011. p-value(Down Syndrome vs. Normal)
- Select OK to generate a Volcano Plot tab for genes in the ANOVA spreadsheet (Figure 11)
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