Bioconductor Copy number

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cn.MOPS CNV copy number

5.7 years ago liorglic ▴ 10

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1.9k

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copy number

8.3 years ago mms140130 • 0

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989

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cghcall r cgh copy number

8.5 years ago kitcurtius • 0

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bioconductor ChAMP copy number batch effect normalization

updated 8.6 years ago by rasmus.rydbirk ▴ 10 • written 8.7 years ago by apmishra • 0

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ChAMP champ copy number

8.8 years ago apmishra • 0

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CopywriteR copy number

updated 9.7 years ago by t.kuilman ▴ 170 • written 9.7 years ago by smcnulty • 0

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crlmm copy number

10.6 years ago kforner • 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

Votes

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

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

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