DEGseq - 3 conditions
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8 weeks ago
pingu77 ▴ 10

Hello, I am fairly new to DEG analysis.

I have three conditions: A, B, C and I would like to get all the genes that are differentially expressed in A respect to B and C. I am testing DEseq2, should I run it twice? For example: A vs B A vs C

And take the genes that have a significant logFC and pvalue in both, or is there another way for doing this?

Thank you

rnaseq • 239 views
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Add more details about the design. Is something like disease-control-disease+drug? Do you expect that condition B would differ from condition C ?

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thank you for your help! A,B,C are three states of a disease. I would be interested to find the genes that are consistently differentially expressed in A compared to B and C. I expect that not all genes will be the same if I compare A vs B and A vs C but there should be some genes that are DE in both. Should I just take the overlap?

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If samples are indipendent each other, it's fine to have a design column (named here condition) with the three factors (A,B,C) that could be used as design=~condition. So, you'll run:

resB_A <- results(dds, contrast=c("condition","B","A"))
resC_A <- results(dds, contrast=c("condition","C","A"))
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thank you! But after I should take the intersection of the genes that are DE in resB_A and resC_A, right? thank you!

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