[BioC] Problem with Annotation of Mouse4302.db in simpleaffy

[James W. MacDonald]

Hi Marietta,

This appears to be a bug in simpleaffy due to not upgrading to accept 
the new annotation package names. You might try contacting the 
maintainer directly, as he may have missed your questions to the list.

Best,

Jim



Marietta Herrmann wrote:
> Hi,
> 
> I asked this question some weeks ago, but I couldn't solve the problem yet.
> I would be very glad if somebody could help me..
> 
> I tried to use pairwise.comparison in simpleaffy to get a table of results,
> but there is an error with the annotation...
> 
> Thanks for your help,
> 
> Marietta Herrmann
> 
> 
> 
>> data<-ReadAffy()
>> pData<-data.frame(genotype=c(1,1,1,2,2,2), replicate=c(1,2,3,1,2,3))
>> rownames(pData)<-sampleNames(data)
>> vl<-data.frame(c("1 is B6, 2 is D2", "arbitrary numbering"))
>> phenoData(data)<-new("AnnotatedDataFrame", data=pData, varMetadata=vl)
>> library(gcrma)
>> eset<-gcrma(data)
>> library(simpleaffy)
>> results <- pairwise.comparison(eset, "genotype", spots=data)
>> significant<-pairwise.filter(results, fc=log2(2), tt=0.05, present.by.group=T)
> [1] "Checking member 1 in group: ' genotype '"
> [1] "Checking member 2 in group: ' genotype '"
> 
>> summary <- results.summary(significant, "mouse4302")
> Error in library(cdfname, character.only = TRUE) :
>   there is no package called 'mouse4302'
> 
>> summary <- results.summary(significant, "mouse4302.db")
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Error in get(paste(cdfname, "SYMBOL", sep = "")) :
>   variable "mouse4302.dbSYMBOL" was not found
> 
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-apple-darwin9.5.0
> 
> locale:
> de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base 
> 
> other attached packages:
>  [1] mouse4302.db_2.2.5   RSQLite_0.7-1        DBI_0.2-4
>  [4] AnnotationDbi_1.4.1  simpleaffy_2.18.0    genefilter_1.22.0
>  [7] survival_2.34-1      mouse4302probe_2.3.0 mouse4302cdf_2.3.0
> [10] gcrma_2.14.1         matchprobes_1.14.0   affy_1.20.0
> [13] Biobase_2.2.1 
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        annotate_1.20.1      preprocessCore_1.4.0
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662