Bioconductor Multiple testing correction

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IHW multiple testing correction covariate distribution

updated 4.9 years ago by Wolfgang Huber 13k • written 4.9 years ago by lara.h.urban • 0

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qvalue pvalue histogram multiple testing correction

updated 5.3 years ago by Nikos Ignatiadis ▴ 180 • written 5.3 years ago by oliver.selmoni ▴ 10

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limma limma voom limma contrast matrix multiple testing correction

updated 6.6 years ago by James W. MacDonald 63k • written 6.6 years ago by gregory.l.stone ▴ 10

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betr multiple testing correction

7.2 years ago moradzadeh_k921 • 0

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edgeR glmLRT() multiple factor design multiple testing correction

updated 8.7 years ago by Aaron Lun ★ 28k • written 8.7 years ago by Ekarl2 ▴ 80

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Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k

SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…

Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k

The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…

Answer: Remove duplicates of colData in TreeSummarizedExperiment by Michael Love 40k

Copying my code from Slack for posterity. James' code is more streamlined for this step I think. ``` # make a dataset that has duplicate s…

Comment: DataFrame Construction With Non-standard Column by James W. MacDonald 63k

Oh, ok. I understand. Technically both should work according to what the help page for `DataFrame` says (both `SimpleList` and `list` have …

Comment: DeSeq2 design fails (full model matrix is less than full rank) by Basti ▴ 720

As recommended, you can only perform ~group. You can use contrasts do perform the comparison AA5 vs FHIN1 (see [DESeq2 vignette][1]), but t…

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Answer: Further analysis after limma regression output

A: collapseReplicates in DESeq2

Answer: DataFrame Construction With Non-standard Column

Steps needed to change design (relevel factors) in DESeq2

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