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). 

Hi Ilo,

From the RUVSeq vignette:

The normalized values are stored in the normalizedCounts slot and can be accessed with the normCounts method.

The answer to your previous question was also in the vignette. Please, read carefully the RUVSeq vignette before asking questions on the forum.

Best, Davide