Glyco gene chip
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Binita Dutta ▴ 100
@binita-dutta-622
Last seen 9.6 years ago
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. 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
cdf affy cdf affy • 1.2k views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
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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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 >
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