countsFromAbundance for gene-level RSEM import in tximport
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celi0001 • 0
@celi0001-16194
Last seen 3.3 years ago

Hi all,

I’ve used tximport to import RSEM's “*.genes.results”  files and I’ve found that tximport uses the values from RSEM’s "expected counts" regardless of the value specified to the argument “countsFromAbundance” (i.e. “lengthScaledTPM”, “scaledTPM” or “no”). Would I have to correct the expected count values for the average transcript length per gene before I perform a differential gene expression analysis with limma-voom

Thanks, 

Celine

tximport rsem • 572 views
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@mikelove
Last seen 7 hours ago
United States

Thanks for noting this. If you use the latest version of tximport you can provide the isoform files to tximport(), and then you can specify countsFromAbundance of "lengthScaledTPM" or "scaledTPM". I guess I could build out more support to do this from the gene-level files specifically for RSEM, but I like having the clean interface that is mostly built around importing transcript-level data (and we now support RSEM).

I've added a warning to tximport() now if countsFromAbundance != "no" and txIn=FALSE, because it is just importing the data from the gene-level files, and not replacing the counts that RSEM computed.

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I see! Thanks for the quick reply!

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Just realised that, anyway, I should have in fact been using the counts without gene length normalisation for the DEG analysis.

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Hi Love,

I've used tximport to import Salmon "quant.sf" file, and I found there are all "no" at line "countsFromAbundance" in the result file. But I don't know the meaning about "no" at line "countsFromAbundance". Could you please tell me some details? Furthermore, I also found the line "abundance" and "counts" in the result file. What's the exact meaning of "abundance"?

Thanks,

Pan

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For the meaning of "no", you can check the help page, and see the argument countsFromAbundance

?tximport

Abundance is the relative abundance estimated by the tool. This is almost always in units of TPM. For more details on scaledTPM and lengthScaledTPM, take a look at the reference publication listed in ?tximport.

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