Bioconductor DEgenes

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limma deseq2 normalization degenes design and contrast matrix

written 8.4 years ago by mrigaya.mehra ▴ 10

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microarray rnaseq DEgenes meta-analysis limma

updated 8.8 years ago by Aaron Lun ★ 29k • written 8.8 years ago by svlachavas ▴ 840

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Comment: p.adjust BH Question by TikTsoksocissalpc • 0

Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…

Answer: NUPOP usage by shepherl 4.2k

You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…

Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0

In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …

Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150

Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?

Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Votes

C: DESeq2 Following RSEM

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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