Question: Very low EdgeR Pvalues with very small sample size
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gravatar for Venu Pullabhatla
2.9 years ago by
Venu Pullabhatla40 wrote:

Dear EdgeR users

I am working on a RNASeq dataset with extremely small sample size (2 samples in each group; N=4) and I am trying to find any DEG's using these samples (I am aware of the consequences of using very small sample size). I did find some DEG's with P.values as low as 6.9e-17 and an equivalent FDR of 8.14e-13. Although it seems encouraging to see some differences in my samples, I am more concerned about so low P.values with such a small sample size (This is because of my limited statistical knowledge). Just wondering how EdgeR calculates P.values with such low sample sizes. Any comments or opinions are greatly appreciated. Many thanks for your help.

Best

Venu

edger sample size pvalue • 706 views
ADD COMMENTlink modified 2.9 years ago by Aaron Lun23k • written 2.9 years ago by Venu Pullabhatla40
Answer: Very low EdgeR Pvalues with very small sample size
2
gravatar for Aaron Lun
2.9 years ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

The calculation depends on the type of analysis you performed with edgeR. P-values are calculated using the exact test for classic edgeR, the likelihood ratio test for GLMs, and the quasi-likelihood F-test for QL-based analyses. If you want more details on how each of these work, have a look at the corresponding papers that are referenced in ?exactTest, ?glmLRT or ?glmQLFTest.

Generally speaking, getting very low p-values with small sample sizes is not an issue. If you have counts of 1000 in one group and 0 in the other group, then obviously you'll get very low p-values. Remember that edgeR also shares information across genes to improve the stability of the dispersion estimates. This mitigates the loss of power due to small numbers of replicates in typical RNA-seq experimental designs.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Aaron Lun23k
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