I am trying to run DESeq2 package in R. After running the package I have few questions. I will start with this.
baseMean : It is defines as average of the normalized count values, dividing by size factors, taken over all samples in the DESeqDataSet
After this step of the analysis,
ddsMat <- DESeqDataSetFromMatrix(count, colData, design=~condition
ddsMat <- DESeq(ddsMat)
In the above calculation I see estimating size factors
I want to know how I can get estimating size factors. What I want to do is to confirm the value of baseMean generated in the table for a particular gene.
How can I do this?