Question: DESeq2: Small treatment group, large control group
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gravatar for kel.chee86
6 months ago by
kel.chee860
kel.chee860 wrote:

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 • 174 views
ADD COMMENTlink modified 6 months ago by Michael Love24k • written 6 months ago by kel.chee860
Answer: DESeq2: Small treatment group, large control group
0
gravatar for Michael Love
6 months ago by
Michael Love24k
United States
Michael Love24k wrote:

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.

ADD COMMENTlink written 6 months ago by Michael Love24k

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?

ADD REPLYlink modified 6 months ago • written 6 months ago by Steve Lianoglou12k

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!

ADD REPLYlink written 6 months ago by Michael Love24k

I found it just by scrolling through DESeq2 posts:

Question regarding class imbalance and low sample size for DESeq2

ADD REPLYlink written 6 months ago by Michael Love24k
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