Biostar Linear models

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119

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deseq2 design matrix multi-confounders linear models rna-seq

updated 15 months ago by Michael Love 33k • written 15 months ago by mohamedrefaat.1.1992 • 0

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146

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methylation ComBat Linear models batch correction AIC

updated 18 months ago by Kevin Blighe 3.1k • written 18 months ago by lucasmiranda42 • 0

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238

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Limma R Linear Models

updated 2.3 years ago by Aaron Lun ★ 26k • written 2.3 years ago by christiangriffioen • 0

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397

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ballgown linear models

3.2 years ago Yong Li ▴ 50

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835

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microarray SVA ComBat Linear models Residuals

3.9 years ago DataFanatic • 0

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Comment: Determining number of genes in each module based on color in WGCNA package by schum266 • 0

For anyone who might be interested. I was able to figure this out. It's very easy.... just set numericLabels = FALSE. (*sigh*) ``` net = …

Comment: Research fellow in immunology by ATpoint ▴ 640

Try starting a new R session and then load the package again. If that fails then manually install ellipsis version 0.3.2 or greater. By the…

Answer: Creating the correct model to account for paired-samples (patient-effect) help n by Gordon Smyth 43k

In the limma User's Guide, Section 9.4.1 *Paired Samples* covers paired designs. In the edgeR User's Guide, it is Section 3.4.1.

Comment: How to convert .CEL file to .VCF file? by jesus • 0

Thank you! I'd already seen it, but the problem is that I'm using Windows and I think that code is only for Linux. Thanks anyway!

Comment: DESeq2 codes by Ram ▴ 60

DESeq2 is a piece of software that can be used to find statistically significant differential expression in RNAseq datasets. See: https://b…

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Comment: What is the correct use of removeBatchEffect's design parameter

Answer: DESeq2 for allele-specific expression with contrasts between conditions

C: DESeq2 question about use of DESeqDataSetFromTximport() from RSEM data

Comment: Data input for aracne2regulon function in viper package

Comment: DESeq2: NA's in mcols(object)$betaConv

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