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