Bioconductor Normalisation

Showing : normalisation • reset

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895

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DESeq2 Normalisation Bulkrnaseq Svaseq

16 months ago BioinfGuru ▴ 70

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870

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DESeq2 median-of-ratios normalisation

2.5 years ago msrch • 0

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1.5k

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normalisation DESEQ2

updated 4.2 years ago by swbarnes2 ★ 1.4k • written 4.2 years ago by xavier • 0

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4.2k

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deseq2 StringTie RNA-seq normalisation

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by JindrichK • 0

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1.8k

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DESEQ2 circRNA normalisation

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by zoe.ward • 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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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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