Dear list,

Tried to re-analyze an HTqPCR object from last year, but my limmaCtdata command in my R file failed where it worked OK last year. Running the R code that is coming with the package using R studio I noticed that certain modifications of the HTqPCR object "raw" results in the same probem when trying to do linear modeling of microarray data. FilterCtData to  remove genes with 4 or more "Undetermined" features, and change the order according to featureNames (sr.norm2 <- sr.norm[order(featureNames(sr.norm))]) both result in the same error message;

Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 192, 0

Did anyone encounter the same problems with this package and does anyone has a solution to the problem? I'd really like to reanalyze my previous data using this package, but I'm not that good in writing R script files. 

> sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] HTqPCR_1.30.0       RColorBrewer_1.1-2  Biobase_2.36.2      BiocGenerics_0.22.1 limma_3.32.10      

loaded via a namespace (and not attached):
 [1] gtools_3.5.0          bitops_1.0-6          affy_1.54.0           stats4_3.4.0          KernSmooth_2.23-15    BiocInstaller_1.26.1 
 [7] gplots_3.0.1          zlibbioc_1.22.0       gdata_2.18.0          affyio_1.46.0         preprocessCore_1.38.1 statmod_1.4.30       
[13] tools_3.4.0           compiler_3.4.0        caTools_1.17.1

Cheers,

Henk