importing RSEM data into DESeq2
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@dequattroconcetta-21510
Last seen 5 months ago
Italy

Hi! I have performed the transcript abundance quantification with RSEM and then I created the gene-level count matrices for use with DESeq2 by importing the quantification data using tximport following the vignette (http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Importtranscript-levelestimates):

txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)
txi.rsem$length[txi.rsem$length == 0] <- 1
ddsTxi <- DESeqDataSetFromTximport(txi.rsem, colData = samples, design = ~ condition)

I was wondering if this approach corrects by default for potential changes in gene length across samples (e.g. from differential isoform usage).

Thank you, Concetta

deseq2 tximport • 243 views
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@mikelove
Last seen 1 day ago
United States

Yes it should.

When you run DESeq() it should even print out a message, along the lines of, "using average transcript length when estimating size factors..."

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