I am trying the software affy. I follow the user manu of affy and put all the cel files in the working directory. But when i use the rma command, there are many warning messages. for example, cannot open: HTTP status was '404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping I check the web: http://www.bioconductor.org/CRANrepository it was really "404 not found". The attached file has a print out of the warning message. Can you tell me what should I do in order to use affy? Thanks a lot! Zeny

What is happening is that you need something called a cdf environment. It is basically and R package with the name CHIPNAMEcdf, like hgu95av2cdf. Affy sees that this package is not installed and tries to download and install it for you. Apparently something went wrong. You could try downloading the package manually and install it yourself from the bioconductor website. There you'll also find a listing of existing packages in case you are uncertain about the name. Look for "Metadata". /Kasper On Jul 7, 2006, at 7:22 AM, Zeny Feng wrote: > > > I am trying the software affy. I follow the user manu of affy and > put all the > cel files in the working directory. But when i use the rma > command, there are > many warning messages. for example, > > cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/CRANrepository does not seem to > have a valid > repository, skipping > > I check the web: http://www.bioconductor.org/CRANrepository > it was really "404 not found". > > The attached file has a print out of the warning message. > > Can you tell me what should I do in order to use affy? > > Thanks a lot! > > Zeny > > _______________________________________________ > 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

Zeny Feng <zeny.feng at="" yale.edu=""> writes: > I am trying the software affy. I follow the user manu of affy and put all the > cel files in the working directory. But when i use the rma command, there are > many warning messages. for example, > > cannot open: HTTP status was '404 Not Found' > Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid > repository, skipping > > I check the web: http://www.bioconductor.org/CRANrepository > it was really "404 not found". > > The attached file has a print out of the warning message. > > Can you tell me what should I do in order to use affy? Please tell us the version of R and of the affy package that you are using as well as the operating system. I suspect you have an old version and that your problems will be resolved by installing the current release of R and BioC. + seth