DESeq2: Small treatment group, large control group
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kel.chee86 • 0
@kelchee86-18774
Last seen 6.0 years ago

Hi I would to use DESeq2 to analyse NanoString miRNA expression data. I have a group of 5 - 6 conditioned group, and large set of controls available for comparison (>96). In this case I'm looking at different expression between two cancer types. If I include all cases in one analysis, how reliable would the results be? I also think about  breaking the controls into groups of 5-6 cases and perform multiple analysis to have equal size of conditioned and control groups. Would this work? Thanks!

 

 

 

deseq2 sample size • 1.0k views
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@mikelove
Last seen 4 days ago
United States

This question was asked very recently on the site, but it’s hard to find similar questions. My answer was that it’s not technically a problem although the more samples in the small group the better obviously.

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Searching through google with a site:support.bioconductor.org modifier(?) is almost always better than using the search functionality baked into this board. For instance, googling for: unbalanced groups rnaseq site:support.bioconductor.org gets you a few hits:

They all speak to this problem ... maybe the first one was the one you were thinking of?

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I think it’s not in that list... it’s tricky to even think of the possible variations on keywords to find it. Not an easy solution to find related content on forums!

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I found it just by scrolling through DESeq2 posts:

Question regarding class imbalance and low sample size for DESeq2

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