Hi,
I've a question concerning DESeq2. I've a multi-factor design as follow :
samples condition type
Sample_A1 untreated X
Sample_A2 untreated X
Sample_A3 untreated Y
Sample_A4 untreated Y
Sample_B1 treated X
Sample_B2 treated X
Sample_B3 treated Y
Sample_B4 treated Y
so I do
dds <- DESeqDataSetFromHTSeqCount(sampleTable=samples,directory="./",design= ~ type+condition)
dds <- DESeq(dds)
res <- results(dds)
In the results, I wonder how the log2foldchange is computed ? How it takes into account this two-factor design ?
Thanks
•
written
by
Nicolas Rosewick
The two factor design is taken into account as with normal linear regression: we have a term which represents the changes due to type, and a term which represents the change due to condition. Then when you call results(), it is by default testing the condition treated vs untreated effect. But you could also test the type Y vs X effect (more on this in the vignette).
•
written
by
Michael Love
So in my code the foldchange in the results will only take the factor "condition" into account?
•
written
by
Nicolas Rosewick
It's "log2 fold change of the condition while controlling for type".
•
written
by
Devon Ryan
No. It is testing the condition term, but the design includes type, so the type effect is "taken into account" or "controlled for" in the model. You might want to check a reference on linear models for further reference on how this work.
•
written
by
Michael Love
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