Differential gene expression analysis with data matrix generated with RSEM
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ubjw24 • 0
@6bd8ba1e
Last seen 20 days ago
United States

Hi,

I have gene expression matrix downloaded from DepMap data portal (e.g. OmicsExpressionGenesExpectedCountProfile.csv). Basically, it is a data matrix with values generated from RSEM. Row IDs are gene names and column IDs are samples (cell lines). The values are floating type, not integer. I wonder if there is a way to use DESeq2 to perform differential gene expression analysis?

Thanks,

Jason

DESeq2 edgeR • 142 views
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@gordon-smyth
Last seen 6 hours ago
WEHI, Melbourne, Australia

You have included an edgeR tag so I'll answer for edgeR. edgeR will accept floating point (fractional counts) without any isues using a continuous generalization of the negative binomial distribution. For DESeq2 see Mike Love's answer here: Deseq2 raw counts input as integers.

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@mikelove
Last seen 5 hours ago
United States

For DESeq2 just round to integer values.

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Hi Gordon and Michael, thanks for your quick replies.

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