Question

The number of controls versus treatment in differential expression analysis

0

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AZ ▴ 30

@fereshteh-15803

Last seen 12 months 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 • 640 views

ADD COMMENT • link updated 2.1 years ago by Gordon Smyth 50k • written 2.1 years ago by AZ ▴ 30

score 3 · Accepted Answer · 2022-03-18

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Michael Love 41k

@mikelove

Last seen 1 hour ago

United States

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

ADD COMMENT • link 2.1 years ago Michael Love 41k

score 3 · Accepted Answer · 2022-03-18

3

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Gordon Smyth 50k

@gordon-smyth

Last seen 9 hours ago

WEHI, Melbourne, Australia

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

ADD COMMENT • link 2.1 years ago Gordon Smyth 50k