Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
1
0
Entering edit mode
@8d7b51c7
Last seen 12 months ago
Germany

Hi fellow DESeq'ers!

I have a dataset of 180 RNA-seq samples for which I run differential expression analysis using deseq2! I have a mixed up of paired samples and unpaired samples: 60 paired samples (30 cases vs 30 controls from 30 patients) and 120 samples unpaired from 120 patients either case and control! I am wondering if I can use the paired analysis offered by deseq2 in this case ? here is my fomrula

formula(~ sequenicng_lane + Patient_id +  status)

Thanks in advance; Fatemeh

DESeq2 RNAseq123 • 482 views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.0k
@atpoint-13662
Last seen 18 hours ago
Germany

Please see DESeq2: paired samples + controls

ADD COMMENT
0
Entering edit mode

Thanks. I already saw this but there, the question is somehow different in my case most of the samples are unpaired and they are either case or control!

ADD REPLY

Login before adding your answer.

Traffic: 609 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