The authors of CibersortX mainly used TPM in their analysis as the unit of gene expression in samples (Supplementary table 1 in article)
The High-Resolution feature in CibersortX outputs deconvolution values per-gene per-sample, in theory making it possible to test for differential expression. However, TPM units are not recommended for differential expression.
So it is "good" to use TPM as input for CibersortX, but "bad" to use it for differential expression following it.
Is using TPM units both as input for CibersortX and for DE following it - best practice? Is there a better alternative?
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written
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Aspire
1 answer
Yes, TME values cannot be used for Differential gene expression via DESeq2, but you can opt for Kruskal wallis test or Wilcoxon rank-sum tests which are non-parametric test . It means they utilise ranks rather than actual values, so they can be useful with CIBEROSRTx Hi res module output.
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