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  • Differential expression when working without any replicates

    Hi,

    This is a question regarding the DESeq (ver 1 or 2) package.
    I wanted to know if we need to call estimateSizeFactors() when no replicates are available.
    In the DESeq documentation (ver 1 ) , in the section of
    "Working without any replicates", the estimateSizeFactors() is skipped .
    I could also see a post which suggested to work with rlogTransformation() to estimate the rLogFC (no pvalues), where no count normalization was done.
    In the estimateSizeFactors documentation - it is written that the normalization is done over all samples (and not conditions).

    Can anyone elaborate?

    Thanks
    bel.

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