Hi,

I'm using the function RUVg in the RUVSeq package to analyse my RNA-seq data. The output of RUVg consists of the factors of unwanted variation W and the normalised counts N. Could someone please tell me how the normalised counts N are calculated? See the formula below.

log E[Y |W, X, O] = W α + Xβ + O.

Are the normalised counts simply log(Y)-Wα-O? If so, how can I get α from the output of RUVg? Also, log(Y)-Wα-O wouldn't consist of integers, so why does the normalised counts matrix N produced by RUVg consist of counts?

Thanks!

Paul

Hi Chris,

please, use the "Add Answer" field only to answer the original posted question. If you have a new question, please open a new thread.

In this particular case, it looks like the best place for you to start is by reading the RUVg vignette, available here:

https://www.bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf

Hi David,

Many thanks for your quick reply.

I did start with the RUVSeq vignette, but i can't find how to export the normalized counts? I have got a kinetics data and I dont know how to apply DESeq on such a data. Hence, I would like to export the RUVg normalized data frame.

Thanks,

Chris

The way you extract normalized counts depends on what object you're working on. If you're starting with a matrix, RUVg will return a list with two elements, one of which is the matrix of normalized counts.

If you're working with a SeqExpressionSet object, then you can use the normCounts() method to extract the normalized data. This is all documented in the RUVg manual page, available with:

Have a look also at