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isoNorm applies a different normalization function #26

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bounlu opened this issue Dec 7, 2023 · 0 comments
Open

isoNorm applies a different normalization function #26

bounlu opened this issue Dec 7, 2023 · 0 comments

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@bounlu
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bounlu commented Dec 7, 2023

The documentation says isoNorm function applies DESeq2::rlog() function but the code applies DESeq2::varianceStabilizingTransformation() function instead:

isomiRs/vignettes/isomiRs.Rmd

Line 178 in 8f953e5

The normalization uses `rlog` from `r Biocpkg("DESeq2")` package and

isomiRs/R/isomiRs.R

Line 439 in 8f953e5

rld <- varianceStabilizingTransformation(dds, blind=FALSE)

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