Importing data into the DESeq2 pipeline using tximport
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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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Last seen 4 minutes ago
United States

Not equivalent.

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:

In particular:

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

Entering edit mode

Got it. Thank you so much!


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