Deseq2 Etc. Unequal Sample Sizes
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9.1 years ago
Phil S. ▴ 700

Hi there,

I got an RNA-seq experiment where I have 8 control and 16 case samples sequenced. Can I use DESeq2 and/or similar tools to discover DE genes without further accounting for the different group sizes(case dbl as large as control) or do I have to account for this somehow? If so, what can/should I do?

Thanks in advance,

Phil

statistics r sequencing • 3.3k views
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Hi Devon,

I am facing the same problem. I have 10 control and 48 case samples. I have used all the samples for the analysis with DESEQ2 but I obtain aprox. 3000 DE genes. I think that this high number is because of the unequal sample size. How can I deal with this situation? Is there a way to "correct" by this?

Thanks you a lot,

Teresa

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Entering edit mode

Please don't resurrect 5 year old threads, instead post things like this as a new question.

With 58 total samples you have quite a bit of power, so if you need a smaller list of genes for further analysis then start filtering by fold-change.

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Entering edit mode
9.1 years ago

You can use things as are.

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