Hi all,

I created an object of qPCRset class reading TLDA qPCR plates. I used three different characters to flag my Ct values; Passed, Flagged and Unreliable. All Undetermined and NA values are set to 40 in the qPCRset object. Using the setCategory in HTqPCR I tried to have those Ct values flagged as Unreliable be counted as "Unreliable" in the Category "Unreliable" using  MyqPCRset.cat<-setCategory(MyqPCRset, groups=NULL, flag=True, flag.out="Unreliable", Ct.max=35, replicates = FALSE, verbose = TRUE). I keep ending up with only two categories; "OK", and "Undetermined". Anybody has any idea where I go wrong or is there a bug in this function?

>sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] HTqPCR_1.24.0       limma_3.26.9        RColorBrewer_1.1-2  Biobase_2.30.0     
[5] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] gtools_3.5.0          bitops_1.0-6          affy_1.48.0          
 [4] stats4_3.2.0          KernSmooth_2.23-15    BiocInstaller_1.20.3 
 [7] gplots_3.0.1          zlibbioc_1.16.0       gdata_2.17.0         
[10] affyio_1.40.0         preprocessCore_1.32.0 tools_3.2.0          
[13] caTools_1.17.1       

Henk