Dear there,

I followed the code here for CNV-expression association analysis, but got an error below for cnvEQTL. Why don't they get the error in the linked workshop?

res <- cnvEQTL(cnvrs = "01_GBM_GISTIC_Peaks-20160128", 
               calls = "01_GBM_CNVSNP-20160128", 
               rcounts = "01_GBM_RNASeq2GeneNorm-20160128_ranged", 
               data = gbm, window = "1Mbp", verbose = TRUE)

harmonizing input:
  removing 154 sampleMap rows not in names(experiments)
Preprocessing RNA-seq data ...
Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed

It seems it is "NAs" in read counts that cause the error. So, I remove the NAs. But, it still does't figure the problem out.

Thank you so much!

rmNAgeneName <- rownames(na.omit(assays(gbm)['01_GBM_RNASeq2GeneNorm-20160128_ranged'][[1]]))
gbmRNAnoNA <- gbm[[3]][rownames(gbm[[3]]) %in% rmNAgeneName,]

res <- cnvEQTL(cnvrs = "01_GBM_GISTIC_Peaks-20160128", 
               calls = "01_GBM_CNVSNP-20160128", 
               rcounts = gbmRNAnoNA, 
               data = gbm, window = "1Mbp", verbose = TRUE)

harmonizing input:
  removing 154 sampleMap rows not in names(experiments)
Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE,  : 
  invalid [[ subscript type: RangedSummarizedExperiment