CPM or TPM in GSEA analysis
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22 months ago
francesca3 ▴ 70

Dear all, I have a question. It is better to perform this analysis using CPM or TPM values? Other times I performed this analysis using TPM. This time I have the replicate values only for CPM, while for TPM I have only the mean for each condition. Which is the best way?

Thanks Francesca

RNA-Seq GSEA • 2.4k views
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Which tool are you using? When I use FGSEA, I pass in a differential-expression summary statistic, rather than values from individual samples. For a given gene, the statistic I use is (-log10 of unadjusted p-value) * (sign of differential expression coefficient).

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Entering edit mode
22 months ago
benformatics ★ 2.6k

For most intents and purpose TPM is superior to CPM (at least for short read RNA-seq; where the length of a given transcript affects the number of reads produced from said transcript). However, CPM should give comparable results to using TPM. In your case, I would try both and compare the results.

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22 months ago

Use TPM. CPM are not normalized for gene length length meaning longer genes will appear more highly expressed when using CPM (and vise versa).

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