Nesting a covariate for differential expression design
0
0
Entering edit mode
7 weeks ago
RNAseqer ▴ 150

Hello all,

I would like to create a design for differential gene expression analysis along the lines of

model.matrix(~0 + group + sex + batch)

but one where 'batch' is a nested variable that takes into account the library preparation batch, and the fact that some samples were re-run and the data combined to generate an adequate number of counts, AND the particular flow cells the one (or two) runs of each sample were performed on.

I have not used such a nested design before and though there is some good material I have found on the subject I am still unsure exactly how to encode such a complex nesting variable. I would very much appreciate any advice or examples that more experienced readers could provide.

Many thanks in advance!

RNA-Seq nested covariates • 128 views
ADD COMMENT
0
Entering edit mode

If you ran the exact same library more than once, just combine the counts. It's not a significant source of technical artifacts. Neither is flowcell.

ADD REPLY

Login before adding your answer.

Traffic: 1778 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