Bioconductor Blocking

Showing : blocking • reset

vote

replies

1.9k

views

limma repeated measurements blocking random effects

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by Jane ▴ 10

votes

replies

3.6k

views

limma edger blocking paired samples

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by anou ▴ 10

votes

replies

922

views

diffbind blocking model

updated 3.5 years ago by Rory Stark ★ 5.2k • written 4.5 years ago by melnuesch ▴ 10

votes

806

views

diffbind differential binding analysis blocking

updated 6.3 years ago by Rory Stark ★ 5.2k • written 6.3 years ago by zhangly811 • 0

votes

replies

1.4k

views

edger limma paired blocking ruvseq

updated 3.9 years ago by Gordon Smyth 50k • written 3.9 years ago by ScA • 0

vote

693

views

edgeR blocking

updated 3.0 years ago by Yunshun Chen ▴ 840 • written 3.0 years ago by Molly • 0

votes

replies

688

views

voom blocking limma

updated 6 months ago by Gordon Smyth 50k • written 6 months ago by Gerhard Thallinger ▴ 180

7 results • Page 1 of 1

Recent ...

Replies

Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Votes

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

Awards • All

Supporter to JKim • 0