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Tom
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@tom-10763
Last seen 2.2 years ago

Dear all,

In the vignette of GAGE pathway analysis package, a joint workflow with DESeq2 is shown, where only the column of log2 fold change from DESeq2 output is used as an input for GAGE.

Is rlog matrix calculated by DESeq2 applicable as an input for GAGE pathway analysis?

Any comments would be appreciated.

Best,

Tom

The idea of the vst() and rlog() functions in DESeq2 is to stabilize the variance of transformed counts across the range of values. These two functions are a motivated, statistical approach to transformation rather than picking either an arbitrary psuedocount and/or filter threshold for each dataset which will reduce the large noise component of log(count + x).

vst() and rlog() return data which is log2-like, but the variance has been stabilized for low counts, and should be appropriate for downstream usage.