Bioconductor Private

Showing : private_germline • reset

0

votes

6

replies

1.5k

views

PureCN private_germline mutation_burden

6.5 years ago twtoal ▴ 10

1 result • 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

Awards • All

Popular Question to Talip ▴ 10

Popular Question to alexandre.blais ▴ 50

Popular Question to Fred Hutch (Recruiting) ▴ 40

Locations • All

United Kingdom, 3 minutes ago

The Netherlands, 7 minutes ago

United States, 10 minutes ago

Italy, 12 minutes ago

United States, 18 minutes ago

Traffic: 922 users visited in the last hour

Content Search
Users
Tags
Badges

Help About
FAQ

Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the

version 2.3.6