Hi, I am trying to normalize 64 High Throughput Affy Human arrays in Bioconductor using GCRMA package. One of the hurdles in running justgcrma() is under MetaData section on Bioconductor site I didn't find the HT_Hgu133A cdf and probe files. Does anybody has any clue. I was able to download the HT_Hgu133A cdf file from the Affy Netaffx site but don't know how to make a package out of it that would run on Bioconductor. Any help on this matter will be highly apprecaited. Thanks, Sanchita P.S. Error message as follows: > normalized<-justGCRMA() Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment hthgu133acdf was not found in the Bioconductor repository." [1] "Checking to see if your internet connection works..." [1] "Environment hthgu133aprobe was not found in the Bioconductor repository." Error in get(x, envir, mode, inherits) : variable "hthgu133aprobe" was not found

Hi Sanchita, sanchita at MIT.EDU wrote: > > Hi, > > I am trying to normalize 64 High Throughput Affy Human arrays in Bioconductor > using GCRMA package. > > One of the hurdles in running justgcrma() is under MetaData section on > Bioconductor site I didn't find the HT_Hgu133A cdf and probe files. Does > anybody has any clue. > > I was able to download the HT_Hgu133A cdf file from the Affy Netaffx site but > don't know how to make a package out of it that would run on Bioconductor. I don't see this file. Can you give me a link? My understanding was that the 133A HT plate simply had 96 133A_v2 chips, so I assumed that you got 96 celfiles when you read the plate, and could use the regular 133av2cdf package. Do you not get 96 celfiles? Best, Jim > > Any help on this matter will be highly apprecaited. > > > Thanks, > > Sanchita > > P.S. Error message as follows: > > >>normalized<-justGCRMA() > > Computing affinities[1] "Checking to see if your internet connection works..." > [1] "Environment hthgu133acdf was not found in the Bioconductor repository." > [1] "Checking to see if your internet connection works..." > [1] "Environment hthgu133aprobe was not found in the Bioconductor repository." > Error in get(x, envir, mode, inherits) : variable "hthgu133aprobe" was not found > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.