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
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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!