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Limma/voom gets 0 DE genes but DESeq2 and edgeR gets >5k DE genes.

Hello all, I have two groups which have 3 replicates and 2 other replicates. All gene number is 8k. When I try limma and Voom, no DE genes were detected. Then I tried DESeq2 and edgeR, they both find more than 5k DE genes. It's very weired for limma/voom. The MA plot from limma and voom looks normal. But I am not sure why no DE genes were detected.

Thanks very much enter image description here

rna-seq differential analysis limma voom tool
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written by yancychy • yancychy

Please show all relevant code that you have used. Otherwise, there is no point in anybody here speculating about what you may have done.

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written by Kevin Blighe Kevin Blighe

For future reference, questions should be submitted under the "Question" post type. The "Tool" post type is for announcing a tool you've developed that may be of use to the community. I have changed it this time for you.

As for your question, we need the code used to run the analysis at minimum to help troubleshoot. Preferably, it'd be a completely reproducible example, though that seems unlikely here.

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written by jared.andrews07 jared.andrews07

1 answer

Thanks Kevin and jared. I find the error is caused by the input samples. The PCA plot shows that one sample in group A is very close to group B. I think I made a mistake for the input samples. I will delete my post. I think my question is not good.

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written by yancychy • yancychy

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