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methylset minfi dmpFinder betaHMM beta

updated 12 months ago by James W. MacDonald 68k • written 13 months ago by neyousha • 0

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converge beta DESeq2

2.4 years ago Ndimensional ▴ 20

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limma limmaGUI beta

3.3 years ago fluentin44 • 0

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dna methylation illimina 450k methylation beta M significance

updated 8.1 years ago by James W. MacDonald 68k • written 8.1 years ago by skids121 • 0

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

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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