import size factors in deseq2 storage object
1
0
Entering edit mode
umut.caglar ▴ 10
@umutcaglar-7472
Last seen 8.4 years ago
United States

Hi

I am kind of new at DeSeq2. And I want to understand how I can play with size factors a bit..

I have a data set dataset composed of multiple conditions. So instead of the example dataset treated vs untreated I have many different conditions (if number is necessary it is 52). I have 3 different samples for each condition. Data is raw RNA counts. I have counts for around 5000 different RNA's.

Say I want to calculate size factors with a different method than estimateSizeFactor function provides. Now I have a vector of 52*3 numbers, corresponding to my size factors and I want to put them into my object.

So is it enough to do

rnaObject=DESeqDataSetFromMatrix(countData = unnormalized_rna_data, 
                                colData = meta_condition, 
                                design = ~ condition)
rnaObject=estimateSizeFactors(rnaObject)
rnaObject$sizeFactors <- mySizeFactorVector

to reach what I want?

Thank you very much

Best regards

 

deseq2 estimatesizefactors • 1.3k views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 1 day ago
United States

it's 

sizeFactors(dds) <- x

With man page:

?`sizeFactors<-`

All man pages:

 help(package="DESeq2",help="html")
ADD COMMENT

Login before adding your answer.

Traffic: 557 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