Bioconductor Confounding

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limma voom continuous interactions confounding

8.3 years ago lanhuong ▴ 20

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edger confounding

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by Victoria • 0

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limma gene expression confounding adjustment paired

9.2 years ago Loodramon • 0

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1.9k

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limma GSA confounding within-pair analysis 450k

9.7 years ago Aileen Bahl ▴ 10

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1.3k

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limma batch effect design matrix microarray confounding

7.7 years ago svlachavas ▴ 840

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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k

hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …

Comment: Problems with oarfish + tximport + swish by Michael Love 43k

I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.

Answer: Problems with oarfish + tximport + swish by Michael Love 43k

> This is fine Did tximeta() print that a matching transcriptome was found?

Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k

> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …

Comment: Biomart and ensembl not working? by James W. MacDonald 67k

``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…

Votes

Answer: Limma Interaction Effect with Covariates

Comment: DESeq2 for single cell pseudobulk processing

C: Limma: how to get same output as topTable but for all the genes ?

A: Processing agilent data by limma

A: Linear regression in DESeq2

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