DESeq2 - correct for nested batch with NA values?
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Ania • 0
@4bba54fc
Last seen 8 weeks ago
United States

HI everyone,

I'm running DESeq2 to identify genes that are differentially expressed between two general phenotypes: fruits and vegetables. Here's my design:

    general          specific          batch
===============================================
1   fruit            apple             apple
2   fruit            apple             apple
3   fruit            pear              pear
4   fruit            pear              pear
5   veggie           cucumber          NA
6   veggie           cucumber          NA
7   veggie           cucumber          NA
8   veggie           cucumber          NA
9   veggie           cucumber          NA

I'm a bit worried about the batch effect nested within the fruit phenotype - is there a way, or should I even bother, to try to correct for the differences between apples and pears? If I correct for "specific", I might accidentally take out the "general" effect. But if I replace cucumber level with NA, as in "batch", DESeq2 won't let me add "batch" to the model as a covariate. I also considered taking out the apple/pear batch separately from fruits only (with limma's RemoveBatchEffect for example), and then compare to veggies. But that almost sounds like I would be artificially amplifying the differences I want to see between fruits and veggies. Any other ideas?

Thank you!

DESeq2 deseq2 • 108 views
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@mikelove
Last seen 4 hours ago
United States

In DESeq2 you cannot compare general while controlling for specific, see this second example:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#linear-combinations

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