Question: DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser
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gravatar for immunogirl2
12 weeks ago by
immunogirl220
immunogirl220 wrote:

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 • 235 views
ADD COMMENTlink modified 12 weeks ago by antonioggsousa1.5k • written 12 weeks ago by immunogirl220
1
gravatar for antonioggsousa
12 weeks ago by
antonioggsousa1.5k
antonioggsousa1.5k wrote:

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 COMMENTlink modified 12 weeks ago • written 12 weeks ago by antonioggsousa1.5k

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

ADD REPLYlink written 12 weeks ago by user_without_id140
1

Hi,

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

António

ADD REPLYlink written 12 weeks ago by antonioggsousa1.5k
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