Bioconductor Fold change

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R deseq2 edger differential gene expression fold change

updated 17 months ago by ATpoint ★ 3.4k • written 5.2 years ago by Beginner ▴ 50

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diffBind Fold Change

updated 2.4 years ago by Joe Nicholas • 0 • written 4.7 years ago by joseluis.ruiz • 0

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edger differential expression genes fold change

updated 4.3 years ago by Aaron Lun ★ 28k • written 4.3 years ago by ilovesuperheroes1993 • 0

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mfuzz fold change log2 STANDARDISATION

5.2 years ago prakashpandey1111 • 0

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ballgown stattest fold change

updated 5.5 years ago by James W. MacDonald 63k • written 5.5 years ago by ag1805x ▴ 80

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edgeR DE analysis fold change cpm

updated 7.1 years ago by Ryan C. Thompson 7.8k • written 7.1 years ago by Sara ▴ 10

7 results • Page 1 of 1

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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