Bioconductor CBioPortalData

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RaggedExperiment cBioPortalData

updated 13 months ago by Marcel Ramos 680 • written 13 months ago by ryan.hagenson • 0

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cBioPortalData

13 months ago ryan.hagenson • 0

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cBioPortalData

updated 11 weeks ago by Ndimensional ▴ 20 • written 2.4 years ago by andreas.wernitznig • 0

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MultiAssayExperiment cBioPortalData

updated 2.4 years ago by Kevin Blighe 3.8k • written 2.4 years ago by Javier • 0

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

Have you checked from the MDS plot that there is a visible batch effect for the repeated samples? Batch correction has lots of negative con…

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…

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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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