Normalized expression set for GSVA

[dzjfeel]

Hi!

I have a NanoString expression set with batch effects detected by RLE and PCA plot. I used RUVSeq to remove batch effects. The codes are as follows:

set <- newSeqExpressionSet(as.matrix(round(raw)), phenoData = pData, featureData = fData)
cIdx <- rownames(set)[fData(set)$Class == "Housekeeping"]
set <- betweenLaneNormalization(set, which = "upper")
set <- RUVg(set, cIdx, k = 1)

I found set contains a dataset which could be extracted by set@assayData[["normalizedCounts"]]. Is it a dataset without batch effects?

According to the protocol of GSVA package, the input of gsva() should be a normalized gene expression dataset. Could the dataset in set be used for GSVA directly? If not, could you please tell me how can I get the normalized dataset for GSVA?

Thank you!