[BioC] Error in GCRMA package

[Hooiveld, Guido]

mmm, after sending my previous email I noticed that the original affy
cdf/sequence files are not aivalable at the U Michigan. I then realized
my co-worker Philip de Groot has prepared a site a while ago at which
all necessary files for the NuGO arrays are available.
http://nugo-r.bioinformatics.nl/NuGO_R.html

G

 

> -----Original Message-----
> From: Hooiveld, Guido 
> Sent: 13 December 2007 19:53
> To: 'H Parikh'; Bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] Error in GCRMA package
> 
> 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/Cust
> omCDF/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
> > 
> > 	[[alternative HTML version deleted]]
> > 
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> >