estimateSizeFactors after subsetting?
1
0
Entering edit mode
@andrebolerbarros-16788
Last seen 6 months ago
Portugal

Hello everyone,

I have a dataset of RNASeq counts for several cell types. For each cell type, I am running a DESeq model for the specific subset. Should I run estimateSizeFactors for each subset or use the global one?

Example:

dds<-DESeq(dds) 
dds_sub<-dds[dds$condition!="CellA",]
dds_sub<-DESeq(dds_sub)

or...

dds<-DESeq(dds) 
dds_sub<-dds[dds$condition!="CellA",]
dds_sub<-estimateSizeFactors(dds_sub)
dds_sub<-DESeq(dds_sub)

Thanks in advance.

deseq2 • 782 views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 4 days ago
United States

I usually use the same size factors estimated on one dataset for all comparisons, likewise the dispersion estimates. See the FAQ in the vignette on this question.

ADD COMMENT
0
Entering edit mode

Thanks Michael, for your response.

I've looked at the vignette, and indeed found the scenario for when to subset. However, in the context of a subset, do the estimateSizeFactors be run a priori, before running DESeq again?

ADD REPLY

Login before adding your answer.

Traffic: 605 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