DE Analysis on Scran-Normalized Counts
1
0
Entering edit mode
10 months ago

I would like to perform differential expression analysis on a scRNA-sequenced GEO dataset (GSE111065). I can use either raw counts from featureCounts, or normalized counts prepared via the deconvolution method in scran. I would like to use the normalized counts if possible, but am unsure if I can use them as input into programs like Seurat. I'm interested in figuring our how a few very specific genes change between cells of different types.

R RNA-Seq scRNA-Seq • 453 views
ADD COMMENT
2
Entering edit mode
10 months ago

If you're already using scran, why don't you just use Bioconductor packages for your DE as described in the OSCA book? Chapters 11 and 14 may be of particular interest to you.

ADD COMMENT
0
Entering edit mode

Thank you! I'll look into those chapters.

ADD REPLY

Login before adding your answer.

Traffic: 1776 users visited in the last hour
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