[BioC] Glyco gene chip

[James W. MacDonald]

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