Bioconductor Batch Correction

Showing : Batch Correction • reset

votes

replies

2.0k

views

scrna-seq integration batch correction

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by p.joshi ▴ 40

votes

1.5k

views

methylation ComBat Linear models batch correction AIC

updated 5.5 years ago by Kevin Blighe ★ 4.0k • written 5.5 years ago by lucasmiranda42 • 0

votes

replies

873

views

DESeq2 batch correction

updated 5.5 years ago by James W. MacDonald 68k • written 5.5 years ago by MT ▴ 10

votes

replies

1.3k

views

Diffbind ATAC batch correction blocking factor

updated 5.8 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by rm1238 • 0

vote

1.2k

views

deseq2 differential expression batch correction design

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by wunderl ▴ 40

votes

replies

1.9k

views

deseq2 differential expression batch correction

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by wunderl ▴ 40

votes

replies

2.4k

views

SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.1 years ago by Vladimir Kiselev ▴ 150 • written 6.1 years ago by hamza_karakurt ▴ 60

7 results • Page 1 of 1

Recent ...

Replies

Comment: parameters of filterByExpr by caroline.zanchi ▴ 10

It worked, I think I finally understand and accept that fact. Sorry and thank you again !

Comment: parameters of filterByExpr by Gordon Smyth 52k

You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…

Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k

modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…

Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k

Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…

Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k

`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …

Votes

Answer: LogFC values in edgeR - w/wo intercept

How to formulate 2 factor nested design in DESeq2

Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm

Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)

Awards • All