Bioconductor Quality

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RNA-seq PCA control DESeq2 Quality

19 months ago • updated 17 months ago 9906201a ▴ 20

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folder quality QualityControl AffyExpress

2.8 years ago bastien_chassagnol • 0

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microarray quality

updated 4.7 years ago by Wolfgang Huber 13k • written 4.7 years ago by RV ▴ 10

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base quality quality mean base quality

updated 7.0 years ago by Mike Smith ★ 6.1k • written 7.0 years ago by christiangriffioen • 0

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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…

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

Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by James W. MacDonald 63k

No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…

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

Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …

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

Answer: Remove duplicates of colData in TreeSummarizedExperiment

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Scholar to James W. MacDonald 63k