Bioconductor Modelmatrix

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limma modelmatrix pairedanalysis Proteomics

written 11 months ago by svlachavas ▴ 840

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limma modelmatrix

updated 13 months ago by Gordon Smyth 53k • written 13 months ago by kyj2226 • 0

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ALDEx2 modelmatrix covariates

2.5 years ago amir • 0

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DESeq2 limma modelmatrix edgeR designmatrix

updated 4.1 years ago by Gordon Smyth 53k • written 4.2 years ago by rebecca.lea.johnston • 0

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interactionterm edgeR modelmatrix

4.9 years ago ahsindoomilup • 0

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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.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

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C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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