Bioconductor Gene expression

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gene expression network cytoscape

7.8 years ago torgeirous • 0

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limma gene expression confounding adjustment paired

10.0 years ago Loodramon • 0

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sva combat gene expression batch effect rnaseq

updated 10.1 years ago by Jeff Leek ▴ 650 • written 10.2 years ago by Farshad Farshidfar ▴ 10

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ggplot2 barplot gene expression gene expression

updated 10.2 years ago by James W. MacDonald 68k • written 10.2 years ago by alakatos ▴ 130

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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

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Comment: DESeq2 interactions by Michael Love 43k

GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …

Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k

We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you

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Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

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