Hello,
I have some trouble understanding how the log2FoldChange is calculated in DESeq2? Assuming that the full model is ~ AF + Condition, I'm interested in the log2FoldChange of the raw counts with respect to the covariate Condition (which is a factor with two levels).
I was under the impression that its calculated as the log2 of the ratio of mean of the normalized counts in the two levels. However, this is not what I get from DESeq2. Could someone please give me a hint on how these values are actually calculated?
Or is there a way I can get an estimate (or values close the log2FoldChange obtained from DESeq2) without using DESeq2?
Thanks,
Golsheed
I have some trouble understanding how the log2FoldChange is calculated in DESeq2? Assuming that the full model is ~ AF + Condition, I'm interested in the log2FoldChange of the raw counts with respect to the covariate Condition (which is a factor with two levels).
I was under the impression that its calculated as the log2 of the ratio of mean of the normalized counts in the two levels. However, this is not what I get from DESeq2. Could someone please give me a hint on how these values are actually calculated?
Or is there a way I can get an estimate (or values close the log2FoldChange obtained from DESeq2) without using DESeq2?
Thanks,
Golsheed
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