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

 

it's 

sizeFactors(dds) <- x

With man page:

?`sizeFactors<-`

All man pages:

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