Importing data into the DESeq2 pipeline using tximport
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@nikolay-ivanov-23079
Last seen 20 minutes ago
USA/New York City/Weill Cornell Medicine

I have a question regarding importing data into the DESeq2 pipeline using tximport.

I’m reading in salmon quant files using txiport:

tx_salmon = tximport(salmonFiles, type = "salmon", tx2gene = tx2, ignoreTxVersion=T)

After that, I make a DESeqDataSet:

dds = DESeqDataSetFromTximport(tx_salmon, colData = metadata, design = ~ condition)

Since tx_salmon$counts gives you un-normalized counts, the code above is absolutely equivalent to:

dds = DESeqDataSetFromMatrix(countData = tx_salmon$counts, colData = metadata, design = ~ condition)

Is that correct? I just wanted to confirm.

Thank you!

DESeq2 tximport • 71 views
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@mikelove
Last seen 4 minutes ago
United States

Not equivalent.

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#transcript-abundance-files-and-tximport-tximeta

In particular, this quote from DESeq2 vignette, see bold section:

"Full details on the motivation and methods for importing transcript level abundance and count estimates, summarizing to gene-level count matrices and producing an offset which corrects for potential changes in average transcript length across samples are described in (Soneson, Love, and Robinson 2015)."

Also read here, from tximport vignette:

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor

In particular:

Note: Do not manually pass the original gene-level counts to downstream methods without an offset.

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Got it. Thank you so much!

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