Hi list, 

I'm using the HTqPCR package to read data, set categories, normalize and so on. However, I'm having problems with the HTqPCR limma function "limmaCtData".

normFilt is a normalized and filtered qPCRset

>>show(normFilt)                                                                                                                                             
An object of class "qPCRset"

Size:  92 features, 19 samples

Feature types:  

Feature names: hsa-miR-140-3p-002234 hsa-miR-143-000466 hsa-miR-214-000517 ...

Feature classes:  

Feature categories: OK, Unreliable, Undetermined 

Sample names: 1 2 3 ...
                                                                                                                            
                                                                                                                                      
>> limmaCtData(normFilt, design=design, contrasts=contrasts, adjust.method="fdr") #, lfc=log2(0), ndups=1, spacing=1)

Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 92, 0
Calls: limmaCtData -> cbind -> cbind -> data.frame
Execution halted

Has anybody experienced this problem?

Session Info is as follows:

R » sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Gentoo/Linux

locale:
 [1] LC_CTYPE=pt_BR.utf8          LC_NUMERIC=C                 LC_TIME=pt_BR.utf8           LC_COLLATE=pt_BR.utf8        LC_MONETARY=pt_BR.utf8      
 [6] LC_MESSAGES=pt_BR.utf8       LC_PAPER=pt_BR.utf8          LC_NAME=pt_BR.utf8           LC_ADDRESS=pt_BR.utf8        LC_TELEPHONE=pt_BR.utf8     
[11] LC_MEASUREMENT=pt_BR.utf8    LC_IDENTIFICATION=pt_BR.utf8

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

other attached packages:
 [1] xlsx_0.5.7           xlsxjars_0.6.1       rJava_0.9-8          HTqPCR_1.28.0        limma_3.30.13        RColorBrewer_1.1-2   Biobase_2.34.0      
 [8] BiocGenerics_0.20.0  BiocInstaller_1.24.0 setwidth_1.0-4       colorout_1.1-0      

loaded via a namespace (and not attached):
 [1] gtools_3.5.0          bitops_1.0-6          affy_1.52.0           stats4_3.3.2          KernSmooth_2.23-15    gplots_3.0.1          zlibbioc_1.20.0      
 [8] gdata_2.18.0          affyio_1.44.0         preprocessCore_1.36.0 tools_3.3.2           caTools_1.17.1