Bioconductor Adjustment

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1.8k

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limma adjustment voom removeBatchEffect covariates

18 months ago sukeshinik5 ▴ 20

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1.3k

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DEP P.vals adjustment

updated 6.7 years ago by James W. MacDonald 68k • written 6.7 years ago by 826599 ▴ 10

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2.8k

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cell types differential expression adjustment mixtures rnaseq

updated 8.4 years ago by Ryan C. Thompson ★ 7.9k • written 8.4 years ago by aec ▴ 90

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5.6k

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RNA rnaseq Covariate adjustment deseq

updated 9.8 years ago by Michael Love 43k • written 9.8 years ago by sjs0282 • 0

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4.4k

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limma gene expression confounding adjustment paired

10.1 years ago Loodramon • 0

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7.5k

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limma covariate continuous categorical adjustment

updated 10.4 years ago by Gordon Smyth 53k • written 10.4 years ago by sg45653 • 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…

Votes

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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Popular Question to Dario Strbenac ★ 1.6k

Scholar to Nikos Ignatiadis ▴ 180