DeSeq2 Matched Analysis
1
1
Entering edit mode
7 days ago
Andrea ▴ 10

Hi,

I have an issue with my Deseq analysis that I can't solve. I'm trying to see if a clinical treatment can cause changes in RNA expression in human PBMCs. My data are organized as follows:

Data

It's an example since I have a total of 138 sample (69 IDs)

When I run the Deseq command: design = ~ ID + Batch + Comparison

I obtained the error:

Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.

I can't understand why I can't insert the batch as variable.

Thank you.

rnaseq DE Deseq2 • 207 views
ADD COMMENT
0
Entering edit mode
7 days ago
ATpoint 66k

You cannot fit ID and Batch at the same time. Batch1+2 are nested with ID 1,2,3 while batch 3 is neted with ID4+5. Given that this is a paired analysis fitting ~ID+Comparison should be what you need (and is basically the only think you can do). If you fit ~batch+comparison that you lose the pairing information which is probably critical here.

ADD COMMENT
0
Entering edit mode

oh, I see. I avoid the eventual batch effect since I'm doing a paired analysis.

ADD REPLY

Login before adding your answer.

Traffic: 1468 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