Originally posted by masterpiece
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There's also DEXSeq, which does splicing, so at least you can have some consistency in your method. Whatever you do, don't stick with 1.4, as even the authors will tell you, that version was not good.
One thing you mentioned about lab work, I'm assuming you mean qPCR. How do you handle it with fold changes less than 2? I get many genes that DESeq says are differentially expressed, and the fold change might be as low as 1.25, and no one in my lab seems to think I can validate that with qPCR.
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