Open annashcherbina opened 7 years ago
1) limma_voom(counts) -> Model + SVASEQ_vars
2) limma_voom(counts) -> Model + exp(SVASEQ_vars)
3) limma(asinh(tpm))->Model+SVA_vars
4) limma(asinh(tpm))-> Model+exp(SVA_vars)
5) limma(asinh(tpm)- sur vars) 6) limma(asinh(tpm) - exp(sur vars))
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Voom(counts) converts raw counts to log-cpm values:
Raw counts + surrogate variables added to model
1) limma_voom(counts) -> Model + SVASEQ_vars
2) limma_voom(counts) -> Model + exp(SVASEQ_vars)
asinh(tpm) + surrogate variables added to model
3) limma(asinh(tpm))->Model+SVA_vars
4) limma(asinh(tpm))-> Model+exp(SVA_vars)
asinh(tpm) - surrogate variables
5) limma(asinh(tpm)- sur vars)
6) limma(asinh(tpm) - exp(sur vars))
rlog(counts) --> Model + surrogate variables
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rlog(counts) - surrogate variables