NOISeq Batch Correction to RNA-seq data
0
0
Entering edit mode
7.0 years ago

Hello,

I'm working with RNA-seq data with a known batch effect (samples in witch the RNA extraction method differ) and I have tried different programs to count for that effect. But the only one for now that seems to work is the function ARSyNseq from the NOISeq package seeing the PCA after correction.

Now I want to use the data corrected (ARSyNseq returns values corrected for the batch effect and in my case normalized with TMM) in a program such as EdgeR, limma or DESeq2 to find differentially expressed genes (NOISeq returns a lot of DEGs), but EdgeR and DESeq only can be input with unnormalized counts. I would like to ask to the experts from this page if there is a way to use the output from ARSyNseq in limma or another program.

Thanks.

Batch-effect RNA-Seq ARSyNseq limma NOISeq • 2.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 2463 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