Tech Notes
Q. How do I determine which genes are statistically over- or underexpressed?
Statistical evaluation of differential expression, based on the normalized value, is reported in the Gene Inspector window. In the t-test p-value column, a gene associated with a p-value lower than 0.05 is usually regarded as statistically significant, i.e. up- or downregulated compared to an expression baseline of 1 (or 0 in log mode). See our tech note for more details on the t-test p-value.
To isolate genes that are statistically up- or downregulated, select "Filter on Confidence" from the Filtering menu:
- Select the experiment interpretation to be used for the filter. The default experiment is the active one in the main GeneSpring window, Default Interpretation.
- Select "t-test p-value" from the pull-down menu.
- Set the Multiple Testing Correction option, as desired.
- Enter the maximum acceptable p-value (e.g. 0.05).
The number of genes passing the restriction will appear at the top of the interactive window. Click "Save" to make a gene list.
After saving a gene list filtered on confidence, the associated p-value represents the value adjusted by multiple testing correction, thus not necessarily reflecting the p-value in the Gene Inspector window or the Spreadsheet view.
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