Question: edgeR DEG sample size
0
gravatar for jzhan067
9 months ago by
jzhan0670
jzhan0670 wrote:

Hello,

In DEG analysis using edgeR or limma, is there a requirement on the minimum number of samples to compare? Can I just compare 1 treatment against 1 control, each with multiple replicates?

Regards

edger minimum samples • 182 views
ADD COMMENTlink modified 9 months ago by Gordon Smyth39k • written 9 months ago by jzhan0670
Answer: edgeR DEG sample size
2
gravatar for Gordon Smyth
9 months ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

There is no requirement for a minimum number of samples, apart from the requirement that there must be some replication. Since there must be at least two different experimental conditions in order to have something to compare, and there must be more samples than groups in order to have any replication, it follows that the absolute minimum number of biological samples is 3. An example of an absolute minimal experiment would be to compare n=2 treatment samples to n=1 control sample, something that is perfectly possible in edgeR although not something we would recommend as good experimental practice.

If you have multiple replicates for both treatment and control, then you seem set to go.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Gordon Smyth39k

Thanks very much! You answered my question.

ADD REPLYlink modified 9 months ago • written 9 months ago by jzhan0670
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