HTqPCR package: problems with the limmaCtData function
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@frederico-moraes-ferreira-5929
Last seen 4 months ago
Brazil

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       

 

htqpcr • 831 views
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