Bioconductor Confounding

Showing : confounding • reset

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3.2k

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edger confounding

updated 6.4 years ago by Aaron Lun ★ 29k • written 6.4 years ago by Victoria • 0

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1.4k

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limma batch effect design matrix microarray confounding

8.5 years ago svlachavas ▴ 840

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3.3k

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limma voom continuous interactions confounding

9.1 years ago lanhuong ▴ 20

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4.4k

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limma gene expression confounding adjustment paired

10.0 years ago Loodramon • 0

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2.2k

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limma GSA confounding within-pair analysis 450k

10.5 years ago Aileen Bahl ▴ 10

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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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