Bioconductor Ma-plot

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limma Microarray AgilentChip MA-plot Normalization

4.6 years ago FedeXandeR • 0

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ma-plot deseq2

updated 7.2 years ago by Aaron Lun ★ 29k • written 7.2 years ago by vincentpailler • 0

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ma-plot

7.2 years ago vincentpailler • 0

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deseq2 MA-plot

updated 7.6 years ago by Ryan C. Thompson ★ 7.9k • written 7.6 years ago by Mike ▴ 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

Votes

Bioconductor 3.22 Released!

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

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