Bioconductor BiologicalQuestion

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sva BiologicalQuestion

8 months ago bbao ▴ 10

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BiologicalQuestion OmicsMLRepoR

9 months ago Manisha • 0

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AnnotationDbi Annotation annotation BiologicalQuestion

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

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BiologicalQuestion ReactomeGSA BatchEffect

written 14 months ago by Shaimaa Gamal • 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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