Question: HTqPCR: bug in subsetting qPCRset
0
gravatar for Guido Hooiveld
3.0 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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       
>
htqpcr subsetting • 610 views
ADD COMMENTlink modified 2.8 years ago by henrik.seidel40 • written 3.0 years ago by Guido Hooiveld2.5k
Answer: HTqPCR: bug in subsetting qPCRset
0
gravatar for henrik.seidel
2.8 years ago by
henrik.seidel40 wrote:

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

ADD COMMENTlink written 2.8 years ago by henrik.seidel40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 373 users visited in the last hour