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DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser

Hi, Can I use log2(count+1) transformed TCGA htseq counts from Xenabrowser directly for DESeq2 analysis? Or, do i need to reverse transform the data? Please point me out any R script to reverse transform the file. Thanks in advance.

rna-seq r
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updated by antonioggsousa antonioggsousa • written by immunogirl2 • immunogirl2

1 answer

Hi,

I don't think so. DESeq2 only takes absolute raw counts or counts quantified/estimated by salmon, kallisto, etc, (using tximport), not normalized or transformed counts.

António

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written by antonioggsousa antonioggsousa

António, would you have a reference for this? Thank you.

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written by user_without_id user_without_id

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