[BioC] GCRMA: error / warning

[Zhijin Wu]

Thank you for bringing up the problem. The bug is fixed in the devel 
version now.

best,
Jean
Hooiveld, Guido wrote:
>  
> Dear list,
> When executing GCRMA I encounter a problem. I would appreciate if some
> could point out what may be the cause of the error/warning [In
> Yin[subset] = y0.adj :  number of items to replace is not a multiple of
> replacement length.]
>  
> Thanks,
> Guido
>  
>  
>> library(affy)
> Loading required package: Biobase
> Loading required package: tools
>  
> Welcome to Bioconductor
>  
>  
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>  
>> library(limma)
>> library(gcrma)
>>
>> targets <- readTargets("targets_A48.txt")
> 
>> data <- ReadAffy(filenames=targets$FileName,
> cdfname="Mouse4302_Mm_ENTREZG")
>> data
> AffyBatch object
> size of arrays=1002x1002 features (8 kb)
> cdf=Mouse4302_Mm_ENTREZG (16395 affyids)
> number of samples=9
> number of genes=16395
> annotation=mouse4302mmentrezg
> notes=  
> 
>> data.norm <- gcrma(data, fast=FALSE, affinity.source=c("local"))
> Adjusting for optical effect.........Done.
> Computing base-position profiles for probe affinitiesDone.
> Computing affinities.........Done.
> Adjusting for non-specific binding.........Done.
> Normalizing
> Calculating Expression
> Warning messages:
> 1: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 2: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 3: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 4: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 5: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 6: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 7: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 8: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 9: In Yin[subset] = y0.adj :
>   number of items to replace is not a multiple of replacement length
> 
> 
>> sessionInfo()
> R version 2.8.0 (2008-10-20) 
> i386-pc-mingw32 
>  
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>  
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> methods   base     
>  
> other attached packages:
> [1] mouse4302mmentrezgprobe_11.0.1 mouse4302mmentrezgcdf_11.0.1
> gcrma_2.14.1                  
> [4] matchprobes_1.14.0             limma_2.16.2
> affy_1.20.0                   
> [7] Biobase_2.2.0                 
>  
> loaded via a namespace (and not attached):
> [1] affyio_1.10.0        preprocessCore_1.4.0
> 
>  
> 
> ------------------------------------------------ 
> Guido Hooiveld, PhD 
> Nutrition, Metabolism & Genomics Group 
> Division of Human Nutrition 
> Wageningen University 
> Biotechnion, Bomenweg 2 
> NL-6703 HD Wageningen 
> the Netherlands 
> tel: (+)31 317 485788 
> fax: (+)31 317 483342 
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> email:      guido.hooiveld at wur.nl 
> 
> 
> 
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> 
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-- 
------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu