Comments (1)
durenzn
commented on June 28, 2024
For differential expression analysis, people did use count based method like DEseq2 and EdgeR for many years. However, those methods are worse than the simple ranksum test, which take FPKM or CPM as inputs, when the sample size is large. Please see a recent paper from Jingyi Jessica Li’s group: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4
Overall, to perform differential analysis, we just need to use the raw count and normalize it by total read counts, or FPKM/TPM after normalization would work.
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Related Issues (14)
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