About getting DE genes using MAST
Entering edit mode
Last seen 13 months ago

Dear all,

In the Methods section, in the subsection, Testing for differential expression, it is mentioned that a gene is considered differentially expressped if FDR adjusted p-value is < 0.01 and estimated fold-change is greater than 1.5 (on a log2 scale).

For the estimated fold change, does the paper mean that avglogFC > 1.5 or FC > 1.5 and avglogFC > 0.58 (knowing that log2(1.5) = 0.58)?

Also, it is not clear to me how the p-value was calculated?

Thank you Ahmed

MAST • 284 views
Entering edit mode
Last seen 4 months ago

Hi Ahmed,

The code to reproduce the Genome Biology paper is located here, you will have to be running an older version of R and MAST in order for it to run without modification. Looking through the code, it seems we required a log fold change of log2(1.5) = .58. The P value was the "Hurdle" component using a likelihood ratio test.


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