updated 4.6 years ago by
Aaron Lun
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written 4.6 years ago by
hamza_karakurt
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Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
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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
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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
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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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