[BioC] Error in GCRMA package

[Hooiveld, Guido]

Hi Hemang,

First, let me say that I don't know why you get this error message using
gcrma; that is something for the 'real' gcrma-/R-experts... :-) 

However, our group has been involved in designing this array (and the
mouse one; NuGO = European Nutrigenomics Organisation), and as a
consequence we have quite some experience with the analyses of these
arrays. The default (probe sequence + CDF) files provided by affymetrix,
or the remapped (custom) ones (kindly prepared by Manhong Dai et al from
U Michigan
[http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_
download_v10.asp]) work always perfectly fine! So I suggest to use the
CDF files provided at the link above; I guess one of the flavours must
fit your needs...

Regards,
Guido

------------------------------------------------ 
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
email:      guido.hooiveld at wur.nl

 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of H Parikh
> Sent: 13 December 2007 17:36
> To: Bioconductor at stat.math.ethz.ch
> Subject: [BioC] Error in GCRMA package
> 
> Dear All,
> 
> I am getting a following error message when I tried to use 
> gcrma package for a custom design affymetrix genechip.
> 
> I made a nugohs1a520180cdf (custom Affymetrix chip) package 
> using makecdfenv and also a nugohs1a520180cdfprobe package 
> using matchprobes.
> 
> >micro_data = ReadAffy()
> 
> > micro_data at cdfName = "nugohs1a520180"
> 
> >gcrma(micro_data)
> 
> Adjusting for optical
> effect........................................................
> ......................Done.
> 
> Computing affinities.Done.
> 
> Adjusting for non-specific binding.Error in pms[, i] <- 
> GSB.adj(Yin = pms[, i], subset = index.affinities, :
> 
> number of items to replace is not a multiple of replacement length
> 
> 
> sessionInfo()
> 
> R version 2.6.0 (2007-10-03)
> 
> x86_64-unknown-linux-gnu
> 
> other attached packages:
> 
> gcrma_2.11.1 matchprobes_1.10.0
> 
> affy_1.16.0 preprocessCore_1.0.0
> 
> affyio_1.6.1 Biobase_1.16.2
> 
> 
>  I really appreciate your expert help in this matter.
> 
> Thanks,
> 
> Best regards,
> 
> Hemang
> 
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> 
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