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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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cstmm - curate incompatibility #148

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

In the current implementation, the FPKM calculation in curate doesn't use the library sizes before TMM. As a result, curate completely cancels out the normalization by cstmm. https://github.com/kfuku52/amalgkit/blob/22db4f582ff111232429b1ffa0157ee1d8edd51a/amalgkit/curate.r#L867-L870

To fix this problem, I will reorganize cstmm to produce a file for TMM normalization factors in addition to normalized counts, and curate to calculate TMM-FPKM with the TMM normalization factors from cstmm and raw counts and effective lengths from merge.

kfuku52 commented 1 year ago

https://support.bioconductor.org/p/107719/

kfuku52 commented 1 year ago

https://www.biostars.org/p/317701/

kfuku52 commented 1 year ago

https://stackoverflow.com/questions/72472851/r-deseq2-how-use-tmm-normalized-counts-from-edger-in-inputs-for-deseq2

kfuku52 commented 1 year ago

Fixed in https://github.com/kfuku52/amalgkit/commit/803931b159d59a3f20eb866ac253505438b1da5d