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Differential Gene Expression Analysis From TMM normalized counts

Hi,

I understand that DGE analysis software like EdgeR or DEseq take in raw counts as input and then calculated a normalized factor for TMM. The data set I have only has TMM normalized counts and I do not have access to the original counts. Is there a way to bypass EdgeR's internal normalization? Can I use these TMM values for differential expression analysis and if so, how?

Thank You

rna-seq
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updated by Gordon Smyth Gordon Smyth • written by boyinepallyki • boyinepallyki

1 answer

It depends on what you mean by "TMM normalized counts". If you have CPM values or log-CPM values output by edgeR's cpm function, then you could conduct a DE analysis with them using limma. If you don't have the original counts then you cannot use edgeR.

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written by Gordon Smyth Gordon Smyth

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