Question

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

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3.8 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 • 2.2k views

ADD COMMENT • link updated 3.8 years ago by antonioggsousa 3.2k • written 3.8 years ago by immunogirl2 ▴ 20

score 1 · Answer 1 · 2020-07-23

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3.8 years ago

antonioggsousa 3.2k

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

ADD COMMENT • link 3.8 years ago by antonioggsousa 3.2k

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

ADD REPLY • link 3.8 years ago by user_without_id ▴ 150

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Hi,

Please the referenece can be found here: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#input-data

António

ADD REPLY • link 3.8 years ago by antonioggsousa 3.2k