DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser
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2.2 years ago
immunogirl2 ▴ 20

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 • 1.5k views
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2.2 years ago

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

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