[BioC] Glyco gene chip

[M Perez]

Hi,
Taking from the Limma manual "If you have single
channel arrays others than Affymetrix, you will need
to the read the intensity data into your R session
yourself using the basic R read functions such as
read.table. You will need to create a matrix
containing
the log-intensities with rows for probes and columns
are arrays." Anyway you need something similar to a
Gal or cdf file.
Hth
Manuel

 --- "James W. MacDonald" <jmacdon at med.umich.edu>
escribió:

> Binita Dutta wrote:
> > Dear All,
> > 
> > I am trying to analyse Glyco gene chip data using
> biocobductor (affy 
> > package). After loading the data I encounter
> following problem.
> > 
> >   eset<-rma(Data)
> > Warning message:
> > cannot open: HTTP status was `403 Forbidden'
> > Note:
>
http://www.bioconductor.org/repository/devel/package/Win32
> does not 
> > seem to have a valid repository, skipping
> > Note: You did not specify a download type.  Using
> a default value of: Win32
> > This will be fine for almost all users
> > 
> > Error in getCdfInfo(object) : Could not obtain CDF
> environment, problems 
> > encountered:
> > Specified environment specified did not contain
> GLYCOv2a520086F
> > Library - package glycov2a520086fcdf not installed
> > Data for package affy did not contain
> GLYCOv2a520086F
> > Bioconductor - glycov2a520086fcdf not available
> > In addition: Warning message:
> > Failed to read replisting at 
> >
>
http://www.bioconductor.org/repository/devel/package/Win32
> in: 
> > getReplisting(repURL, repFile, method = method)
> >  >
> > 
> > 
> > .cdf file for this chip is not listed on
> affymetrix site.
> > 
> > Please let me know if this data can be analysed
> without using cdf file.
> 
> Unfortunately, no you will not be able to analyze
> these data (using any 
> software I am familiar with) unless you have the cdf
> file. Whomever 
> originally purchased these chips should have the cdf
> file - Affy always 
> gives the cdf for custom chips to the purchaser, so
> you should be able 
> to get the cdf from them. Then all you have to do is
> make either the 
> cdfenv or cdfpackage.
> 
> Best,
> 
> Jim
> 
> 
> > 
> > Thanks in advance.
> > 
> > Binita
> > 
> > 
> > 
> > 
> > 
> > ==============================
> > 
> > Binita Dutta, PhD
> > MicroArray Facility(MAF)
> > UZ Gasthuisberg
> > Onderwijs en Navorsing
> > Herestraat 49, box 816
> > 3000 Leuven
> > Belgium
> > 
> > tel: 32 (0)16 34 79 33
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
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