Dear all,
I am using DESeq2 for a design ~PAIR+GROUP and I obtained for geneX this result:
geneX | |
baseMean | 62.2087194 |
log2FoldChange | -0.33167142 |
lfcMLE | -2.32040851 |
lfcSE | 0.07892334 |
stat | -4.20245054 |
pvalue | 2.64E-05 |
padj | 0.06846016 |
The normalized counts by DESeq2 are these:
geneX | |
groupB | 17.51 |
groupB | 13.94 |
groupB | 31.76 |
groupA | 82.32 |
groupA | 81.39 |
groupA | 146.33 |
Why is it that the log2FoldChange is so different from the lfcMLE? The gene is clearly down-regulated in groupB by a factor>2 and this is not reflected in the log2FoldChange.
Mike I am using version DESeq2_1.10.1, is it too old?
That version is from 2 years ago. I'd recommend -- if you're on a laptop, or have permissions to do so -- download the latest version of R and update your Bioconductor packages (unless you need to stick with the 2 year old version for some reason, ... e.g. an ongoing project where you need to continue working with an old set of packages).