Hello all,

I am trying to repeat actions from the tutorial http://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#statistical-analysis-of-differential-transcript-usage. My actions were:

 library(DEXSeq)
sample.data_kaskad <- DRIMSeq::samples(d_kaskad)
count.data_kaskad <- round(as.matrix(counts(d_kaskad)[,-c(1:2)]))
dxd_kaskad <- DEXSeqDataSet(countData=count.data_kaskad,
                            sampleData=sample.data_kaskad,
                            design=~sample + exon + condition:exon,
                            featureID=counts(d_kaskad)$feature_id,
                            groupID=counts(d_kaskad)$gene_id)

system.time({
  dxd_kaskad <- estimateSizeFactors(dxd_kaskad)
  dxd_kaskad <- estimateDispersions(dxd_kaskad, quiet=TRUE)
  dxd_kaskad <- testForDEU(dxd_kaskad, reducedModel=~sample + exon)
})
#user  system elapsed 
#14.147   0.009  14.168 


dxr_kaskad <- DEXSeqResults(dxd_kaskad, independentFiltering=FALSE)
qval_kaskad <- perGeneQValue(dxr_kaskad)
dxr_kaskad.g <- data.frame(gene=names(qval_kaskad),qval_kaskad)
columns_kaskad <- c("featureID","groupID","pvalue")
dxr_kaskad <- as.data.frame(dxr_kaskad[,columns_kaskad])
head(dxr_kaskad)

library(stageR)
strp <- function(x) substr(x,1,15)
pConfirmation_kaskad <- matrix(dxr_kaskad$pvalue,ncol=1)
dimnames(pConfirmation_kaskad) <- list(strp(dxr_kaskad$featureID),"transcript")
pScreen_kaskad <- qval_kaskad
names(pScreen_kaskad) <- strp(names(pScreen_kaskad))
tx2gene_kaskad <- as.data.frame(dxr_kaskad[,c("featureID", "groupID")])
for (i in 1:2) tx2gene_kaskad[,i] <- strp(tx2gene_kaskad[,i])

stageRObj_kaskad <- stageRTx(pScreen=pScreen_kaskad, pConfirmation=pConfirmation_kaskad,
                             pScreenAdjusted=TRUE, tx2gene=tx2gene_kaskad)


stageRObj_kaskad <- stageWiseAdjustment(stageRObj_kaskad, method="dtu", alpha=0.05)
suppressWarnings({
  dex.padj_kaskad <- getAdjustedPValues(stageRObj_kaskad, order=FALSE,
                                        onlySignificantGenes=TRUE)
})

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

Error in alpha * 100 : non-numeric argument to binary operator

This is amazing, that the same code was working successfully on another dataset just now. I took the same code and replaced the name of the dataset (BA9 with MUSC) and had this error! Of course, this was in another session and all objects were renewed. Could you please help me with stageR problem Error in alpha * 100 : non-numeric argument to binary operator?

Best regards, Poecile