[BioC] error using combineAffyBatch

[Wolfgang Huber]

Dear Mayte,

thank you for the feedback. The problem appears to happen in the 
"combine" method for data frames that is defined in Biobase, this could 
be because of recent changes there that haven't fully been propagated to 
matchprobes::combineAffyBatch, where combine of data frames is used.

Would it be possible for you to make available everything that is 
necessary to reproduce your problem (e.g. also abatch1 and abatch2, or 
any (subset) version of them that produce the problem). The problem you 
report "unfortunately" doesn't seem to happen for the testdata of the 
matchprobes package itself: 
http://www.bioconductor.org/checkResults/2.1/bioc-LATEST/

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Mayte Suarez-Farinas ha scritto:
> Hi,
> 
> I am using combineAffyBatch function from package matchprobes,but I  
> got the following error:
> 
> library(matchprobes)
> res<-combineAffyBatch(list(abatch1,abatch2), probepkg=c 
> ("hgu133a2probe","hgu133plus2probe"), newcdf="hgu133andPluscdf",  
> verbose=TRUE)
> Loading required package: hgu133a2probe
> package:hgu133a2probe	hgu133a2probe	
> package:hgu133plus2probe	hgu133plus2probe	
> 241837 unique probes in common
> Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x 
> [sharedRows,  :
>    invalid 'x' type in 'x && y'
> 
> 
> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-apple-darwin8.10.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets  methods   base
> 
> other attached packages:
> [1] hgu133a2probe_2.0.0    hgu133plus2probe_2.0.0  
> hgu133plus2cdf_2.0.0   affyQCReport_1.16.0    geneplotter_1.16.0
> [6] lattice_0.16-5         annotate_1.16.0         
> AnnotationDbi_1.0.6    RSQLite_0.6-3          DBI_0.2-3
> [11] RColorBrewer_1.0-1     affyPLM_1.14.0          
> xtable_1.5-2           simpleaffy_2.14.05     gcrma_2.10.0
> [16] matchprobes_1.10.0     genefilter_1.16.0       
> survival_2.34          affy_1.16.0            preprocessCore_1.0.0
> [21] affyio_1.6.1           Biobase_1.16.1
> 
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-21 grid_2.6.0