Hello, I have used the RUVg function in RUVSeq to successfully remove the batch effects in my two groups of samples. Both are controls so I am not concerned about removing any biological significance or signal of interest. I have created RLE and PCA plots that have the demonstrated the desired effect, now how do I output a table of these batch effect free normalized counts?
I read here: RNA-Seq, generate batch-free count matrix in davide russo's answer that "the RUVSeq functions return a matrix of normalized counts that are "batch effect free". I would like this matrix output. I have all of the W_1 factors prepared using pData(set2). Thank you for your help!
Note: I used section 2.4 of the RUVSeq vignette to create my newly normalized data, this uses empirical control genes (the top 5000 least significant genes).