Bioconductor Picksoftthreshold

Showing : picksoftthreshold • reset

votes

replies

1.0k

views

wgcna picksoftthreshold scale-free topology co-expression network

6.6 years ago marcantoine.guery • 0

votes

replies

2.1k

views

wgcna picksoftthreshold

6.6 years ago aditi ▴ 20

vote

2.1k

views

wgcna sft picksoftthreshold threshold rnaseq

updated 6.8 years ago by Peter Langfelder ★ 3.0k • written 6.8 years ago by Fabricio Almeida-Silva ▴ 40

votes

replies

1.9k

views

rnaseq wgcna picksoftthreshold

updated 8.1 years ago by Lluís Revilla Sancho ▴ 760 • written 8.1 years ago by divara01 • 0

votes

replies

4.8k

views

WGCNA pickSoftThreshold power RNA-Seq

updated 8.8 years ago by Peter Langfelder ★ 3.0k • written 8.8 years ago by mrodrigues.fernanda ▴ 10

5 results • Page 1 of 1

Recent ...

Replies

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

Awards • All