DESeq2 with small sample size
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jjeang • 0
@cf05ab06
Last seen 5 weeks ago
United States

The DESeq2 workflow calculates a Wald Statistics to then be compared against a normal distribution.

Right now I am working with a data set with a small number of samples (n=3 for each condition, unmatched), and I think the picture would be more clear if I could somehow ask DESeq2 to compare the Wald Statistic to a t-distribution with the appropriate number of degrees of freedom.

Am I correct that this is not yet possible?

Would it be possible to add this feature, or is that an unreasonable ask?

Thanks, I appreciate the community!

DESeq2 • 124 views
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@mikelove
Last seen 4 hours ago
United States

You can do this already, by running nbinomWaldTest with useT and df arguments.

DESeq() is just a wrapper for: estimateSizeFactors(), estimateDispersions(), nbinomWaldTest().