[BioC] error using combineAffyBatch

[Martin Morgan]

Hi Matye, Wolfgang --

I think the error message is trying to say is that a data frame --
probably from phenoData or featureData of one of the AffyBatch objects
abatch1, abatch2 -- contains a column that is a 'factor', and the
'levels' of the two columns do not agree. I'd guess

sapply(pData(abatch1), class)

might point to the likely problem; you'd have to then look at the
levels of the corresponding columns in the pheno- (or perhaps
feature-) data, and straighten them out. It could also be that the
data frames start off ok (same levels) but in the process of
'combine'ing become messed up.

For trouble-shooting, I think you should be able to use 'combine' on
the data frames themselves, and not on the entire AffyBatch.

> df1 = pData(abatch1)
> df2 = pData(abtach2)
> combine(df1, df2)

Martin


Wolfgang Huber <huber at ebi.ac.uk> writes:

> 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
>
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-- 
Dr. Martin Morgan, PhD
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793