Using already normalized counts
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rattray56 • 0
@rattray56-15737
Last seen 4.7 years ago

I was given an excel spreadsheet with already normalized counts. I cannot seem to get DESeq2 to take data either as HTS counts or DESeq data from matrix. Just not sure how to proceed.

deseq2 • 600 views
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@steve-lianoglou-2771
Last seen 13 months ago
United States

The most preferable choice is to go back to the person who sent you the Excel sheet and ask them if you can get the raw counts, instead.

If you can't do that, I think your best bet is to log transform the normalized counts (if they aren't already) and use the "limma-trend" pipeline, which is "standard" limma, but with eBayes(..., trend = TRUE)

You'll find a number of posts on this site that are about roughly similar questions. If you want more detail, you can search for those, but perhaps you might like to start with this one:

https://support.bioconductor.org/p/98820/

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