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Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

I do not follow why calculate TPM from something derived from TPM.

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

Many thanks for clarification. Then only scaledTPM inherits the normalisation by gene length from TPM, while in lengthScaledTPM the featur…

Comment: Batch correction and repeated measures by Gordon Smyth 48k

I mean add the counts, for example by `sumTechReps`. Technical RNA-seq replicates are always combined by summing rather than by "averaging"…

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batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Answer: Batch correction and repeated measures

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