Bioconductor Openprimer

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openPrimeR

written 2.6 years ago by marongiu.luigi • 0

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openPrimeR

updated 6 months ago by Santiago Edilberto • 0 • written 2.6 years ago by marongiu.luigi • 0

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PCRmultiplex openPrimeR

7 months ago Santiago Edilberto • 0

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openPrimeR

updated 6 months ago by Basti ▴ 720 • written 6 months ago by Santiago Edilberto • 0

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Comment: Batch correction and repeated measures by Jonathan • 0

Thank you for your swift answer :)

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction by Gordon Smyth 48k

I am telling you that `LS_B.vs.NL_B` is completely uninteresting. You need instead to examine `LS_Y.vs.NL_Y` and `LS_N.vs.NL_N` separately.

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

You should just do a standard limma analysis as recommended in the previous posts. ``` design <- model.matrix(~0 + Sample.Type + batch) i <…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…

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Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Answer: Batch correction and repeated measures

Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

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