Question: Using altHypothesis with shrunken LFC values in DESeq2
0
gravatar for zefrieira
3 months ago by
zefrieira0
zefrieira0 wrote:

Currently, the only way to use altHypothesis in DESeq2 is through results. However, this doesn't allow to use altHypothesis in shrunken LFC values. I want to isolate genes with low LFC and I'm using altHypothesis="lessAbs" for that, but, as my LFC values were not shrunken, I think I may be underestimating the fraction of genes with low LFC.

deseq2 • 107 views
ADD COMMENTlink modified 3 months ago by Michael Love25k • written 3 months ago by zefrieira0
Answer: Using altHypothesis with shrunken LFC values in DESeq2
2
gravatar for Michael Love
3 months ago by
Michael Love25k
United States
Michael Love25k wrote:

You don't want to use shrunken LFC for when your alternative hypothesis is that the genes are less than theta in absolute value (and the software won't allow this), see the DESeq2 paper for discussion.

ADD COMMENTlink written 3 months ago by Michael Love25k
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