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  • condition of use about RNA-Seq normalisation

    Hi,

    I use 3 tools to analyse RNA-Seq data :
    - edgeR
    - DESeq
    - NOISeq

    Each tool offers several normalisation :
    - TMM (Trimmed Mean of M)
    - RLE (relative log expression) = by default in DESeq ?
    - quantile (edgeR) = Upper Quartile (NOISeq) ? Counts are divided by the third quartile of
    counts for transcripts with at least one read ?

    I know TMM method assume that the majority of gene are not differentially expressed...
    In my case, I analyse data with a lot of gene that are differentially expressed.
    Can I use RLE normalisation with this data ? TMM method is not appropriate.
    I think Upper-Quartile is OK for my case.

    Thank you for your help

    Emeric

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