 
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@wur.nl 



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