[BioC] error using combineAffyBatch

[Mayte Suarez-Farinas]

Hi Martin, Huber and BioC

Martin was right. Now it works!!
thanks very much!!

Mayte

On Nov 26, 2007, at 10:32 AM, Wolfgang Huber wrote:

>
> Dear Martin - thank you, that seems
> Dear Mayte, please let us know if that solves your problem (then we
> don't need to go through the big datafile transfer thing).
>  Best wishes
> 	Wolfgang
>
>
>
>
> Martin Morgan ha scritto:
>> 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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>>
>
>
> -- 
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>