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ramwas bams

updated 7 months ago by James W. MacDonald 63k • written 7 months ago by Anushka • 0

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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"…

Comment: Batch correction and repeated measures by Jonathan ▴ 10

Thanks, I'll try that. BTW, what do you mean by "sum them"? Do you mean averaging them?

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

I see no evidence of a batch effect. I would be tempted to sum the technical replicates and analyse the data without batch correction.

Comment: Batch correction and repeated measures by Jonathan ▴ 10

The technical replicates do look rather similar on the MDS plot, but the axes percentages are rather low... is that enough to draw conclusi…

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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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