Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
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@mohammedtoufiq91-17679
Last seen 9 days ago
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Hi,

I have RSEM expected count, TPM , and FPKM values in a .csv file for all samples (60000 genes 18 samples). I understand edgeR can work with expected counts as output by RSEM, then normalize, and perform differential gene expression analysis between two or more groups.

But I want to avoid normalization process since, I already have the batch corrected TPM and FPKM values, Is there a way in edgeR to import the TMP or FPKM values, and then only perform differential gene expression analysis between groups (OR) limma is the best option to use these values and perform differential gene expression analysis?

Thank you in advance for your help.

Best Regards,

Toufiq

DESeq2 R edgeR Normalization RNASeq • 327 views
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@gordon-smyth
Last seen 5 minutes ago
WEHI, Melbourne, Australia

See Differential expression of FPKM from RNA-seq data using limma and voom()

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Hi Gordon Smyth thank you for the prompt response. I will try this.

Are TPM values supported in limma for differential expression analysis?

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