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=""> escribi?: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >