Hello, using the latest release version of HTqPCR (1.28.0) I experience a problem when subsetting a "qPCRset" object: some of the 'metadata' is lost after subsetting, e.g. the featureType() info. Also the sample names (column names) are lost...

Since I am rerunning an analysis, I know this did NOT occur in the previous versions (1.26.0 and 1.24.0). Anyone knows how to solve this?

Thanks,

Guido

Reproducible example (using included dataset)

> library(HTqPCR)
> data(qPCRpros)
> show(qPCRpros)
An object of class "qPCRset"
Size:  384 features, 6 samples
Feature types:            
Feature names:           Gene1 Gene2 Gene3 ...
Feature classes:                  
Feature categories:      OK, Undetermined, Unreliable
Sample names:            sample1 sample2 sample3 ...
>
> featureType(qPCRpros)[1:5]
[1] "Endogenous Control" "Target"             "Target"            
[4] "Target"             "Target"            
> featureCategory(qPCRpros)[1:5,1:2]
      sample1 sample2
Gene1      OK      OK
Gene2      OK      OK
Gene3      OK      OK
Gene4      OK      OK
Gene5      OK      OK
>
> qPCRpros.subset <- qPCRpros[,1:3]
> show(qPCRpros.subset)
An object of class "qPCRset"
Size:  384 features, 3 samples
Feature types:            
Feature names:           Gene1 Gene2 Gene3 ...
Feature classes:                  
Feature categories:      OK, Undetermined, Unreliable
Sample names:            1 2 3 ...
>
> featureType(qPCRpros.subset)
character(0) #featureType info is lost...
> featureCategory(qPCRpros.subset)[1:5,]
       1  2  3
Gene1 OK OK OK
Gene2 OK OK OK
Gene3 OK OK OK
Gene4 OK OK OK
Gene5 OK OK OK
> # sample names are lost (should be sample1, etc).

NB: the problem reported here may be related to my issue? Errors with HTqPCR v1.28.0 and BioC 3.4

<<edit: oops, I initially copied the wrong link...>>>

> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] HTqPCR_1.28.0       limma_3.30.3        RColorBrewer_1.1-2
[4] Biobase_2.34.0      BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] gtools_3.5.0          bitops_1.0-6          affy_1.52.0          
 [4] stats4_3.3.1          KernSmooth_2.23-15    BiocInstaller_1.24.0
 [7] gplots_3.0.1          zlibbioc_1.20.0       gdata_2.17.0         
[10] affyio_1.44.0         preprocessCore_1.36.0 tools_3.3.1          
[13] caTools_1.17.1       
>

<<edit2: output previous BioC version >>

> qPCRpros.subset <- qPCRpros[,1:3]
> featureType(qPCRpros.subset)[1:5]
[1] "Endogenous Control" "Target"             "Target"            
[4] "Target"             "Target"            
> featureCategory(qPCRpros.subset)[1:5,]
      sample1 sample2 sample3
Gene1      OK      OK      OK
Gene2      OK      OK      OK
Gene3      OK      OK      OK
Gene4      OK      OK      OK
Gene5      OK      OK      OK
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] HTqPCR_1.24.0       limma_3.26.9        RColorBrewer_1.1-2
[4] Biobase_2.30.0      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_3.2.5          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_3.2.5          
[13] caTools_1.17.1       
>

See Subsetting qPCRset loses sample names, possibly due to change of assayDataElementReplace