Bioconductor Overrepresentation

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overrepresentation overlap R hypergeometric

updated 11 months ago by ATpoint ★ 3.4k • written 11 months ago by charles.foster ▴ 160

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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…

Answer: Remove duplicates of colData in TreeSummarizedExperiment by James W. MacDonald 63k

I avoid the tidyverse as a general rule, so cannot give help regarding the use of `distinct`. It does appear to be a re-implementation of t…

Comment: DataFrame Construction With Non-standard Column by ATpoint ★ 3.4k

``` suppressMessages(library(S4Vectors)) DataFrame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8)) #> Error in DataFrame(ID = LETTERS[1:3]…

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

Same reason that `list` works without `I`. Both `data.frame` and `DFrame` objects have an expectation that the resulting object should have…

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A: collapseReplicates in DESeq2

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