The number of controls versus treatment in differential expression analysis
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@fereshteh-15803
Last seen 12 weeks ago
United Kingdom

Hello

I have RNAseq of miRNAs so the number of tested miRNAs are 1640

I have 2 healthy samples versus 12 cancer samples Does it Statistically make sense to compare two controls with 12 cancers?

Can I trust the p-value in differential expression?

Thank you

DESeq2 edgeR limma • 183 views
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@mikelove
Last seen 2 days ago
United States

Yes, this should be fine, I would examine plotDispEsts and also the plotCounts for top genes.

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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Fine, there is no assumption that the groups have equal sample numbers.

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