Biostar Adjustment

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288

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DEP P.vals adjustment

updated 2.5 years ago by James W. MacDonald 58k • written 2.5 years ago by 826599 ▴ 10

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1.5k

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cell types differential expression adjustment mixtures rnaseq

updated 4.2 years ago by Ryan C. Thompson 7.6k • written 4.2 years ago by aec ▴ 70

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3.8k

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RNA rnaseq Covariate adjustment deseq

updated 5.6 years ago by Michael Love 34k • written 5.6 years ago by sjs0282 • 0

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2.5k

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limma gene expression confounding adjustment paired

5.9 years ago Loodramon • 0

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4.8k

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limma covariate continuous categorical adjustment

updated 6.2 years ago by Gordon Smyth 43k • written 6.2 years ago by sg45653 • 0

5 results • Page 1 of 1

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Answer: Microarray - Illumina Metadata by James W. MacDonald 58k

It's not exactly clear to me what you are after, but I'll take a stab at it. First off you probably want to read in using the `GEOquery` pa…

Answer: Can VST be run without runing DESeq or estimateSizeFactors by ATpoint ▴ 850

Just run it, the necessary steps are taken care of internally. You do not have to do anything other than `vst()`.

Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k

Hi, just in case for future users with a similar problem. The package doesn't seem to work with the resources downloaded from the Annotatio…

Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0

EDIT: Ignore this, re-read the warning message in more detail (belatedly). I am now moving the cache. Thanks for the reply, I have since u…

Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Michael Love 34k

See the tidy argument details.

Votes

Answer: DESeq2 fold change filtering

A: Differential expression of RNA-seq data using limma and voom()

A: Differential expression analysis starting from TPM data

Comment: deseq2 machine sizing best practices for very large data set

Comment: Extracting normalized counts in MEDIPS

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