Dear Bioconductor Mailing List, I'm currently trying to run GCRMA on some Hu6800 Affymetrix GeneChip data and keep receiving the following error after I type "eset <-gcrma(Data)": "Please download and install the hu6800probe library from: http://www.bioconductor.org/data/metaData.html". I went to the website and downloaded the probe library file from that webpage but I'm still receiving the error message. I have download other probe library files for other old Affymetrix GeneChip designs and they have worked fine except for Hu35KD which I can't download from the Metadata webpage because the link is bad. Could you great guys and gals at Bioconductor fix the link for the Hu35KD probe library file and find a solution for current problem I'm having between GCRMA and Hu6800 probe library file? Thank you for your time on this matter. David Stiles Technologist NIH/NIDDK Microarray Core Facility Phone: (301) 496-0175 Fax: (301) 480-0855?

> which I can't download from the Metadata webpage because the link is bad. > Could you great guys and gals at Bioconductor fix the link for the Hu35KD > probe library file and find a solution for current problem I'm having The link is now fixed on the website, thanks for pointing that out.

On Wed, Mar 10, 2004 at 03:36:02PM -0500, Stiles, David (NIH/NIDDK) wrote: > Dear Bioconductor Mailing List, > > I'm currently trying to run GCRMA on some Hu6800 Affymetrix GeneChip > data and keep receiving the following error after I type "eset > <-gcrma(Data)": "Please download and install the hu6800probe library from: > http://www.bioconductor.org/data/metaData.html". I went to the website and > downloaded the probe library file from that webpage but I'm still receiving > the error message. I have download other probe library files for other old I think the problem might be due to naming conventions. Somehow the annotation package and cdf packages are called hu6800 but the probe package is called hugeneflprobe - I suspect we need to rename it. Does anyone know in Biocore know if there is a good reason for this naming convention? In most cases you are better off using the internal to R mechanisms for downloading data packages etc. Those include the functions available through the Packages menu on Windows and install.packages2 in the reposTools package from Bioconductor. So something like library(reposTools) install.packages2("pkgnamehere") should work...but in this case it doesn't since hu6800probe does not exist. > Affymetrix GeneChip designs and they have worked fine except for Hu35KD > which I can't download from the Metadata webpage because the link is bad. > Could you great guys and gals at Bioconductor fix the link for the Hu35KD > probe library file and find a solution for current problem I'm having > between GCRMA and Hu6800 probe library file? Thank you for your time on > this matter. > Yep, we're going to fix it - thanks for the report. And we will send you a properly named version of the 6800 probe package if you would be so kind as to tell us your OS (I'm guessing Windows since that was the broken link....) Robert > David Stiles > Technologist > NIH/NIDDK Microarray Core Facility > Phone: (301) 496-0175 > Fax: (301) 480-0855? > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

Hi, I had a similar problem before. After I changed "hu6800" to "Hu6800" in each cell file, it worked fine for me. Yongxing -----Original Message----- From: Stiles, David (NIH/NIDDK) [mailto:DavidST@intra.niddk.nih.gov] Sent: Wednesday, March 10, 2004 2:36 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Problems with Hu6800 and GCRMA... Dear Bioconductor Mailing List, I'm currently trying to run GCRMA on some Hu6800 Affymetrix GeneChip data and keep receiving the following error after I type "eset <-gcrma(Data)": "Please download and install the hu6800probe library from: http://www.bioconductor.org/data/metaData.html". I went to the website and downloaded the probe library file from that webpage but I'm still receiving the error message. I have download other probe library files for other old Affymetrix GeneChip designs and they have worked fine except for Hu35KD which I can't download from the Metadata webpage because the link is bad. Could you great guys and gals at Bioconductor fix the link for the Hu35KD probe library file and find a solution for current problem I'm having between GCRMA and Hu6800 probe library file? Thank you for your time on this matter. David Stiles Technologist NIH/NIDDK Microarray Core Facility Phone: (301) 496-0175 Fax: (301) 480-0855? _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Dear Robert and Bioconductor Support Group, Thanks for the help in fixing my problems with GCRMA and the probe library file for the Hu6800 GeneChip as well as fixing the bad link for the probe library files for Hu35KD GeneChip. Yours truly, David Stiles Technologist NIH/NIDDK Microarray Core Facility Phone: (301) 496-0175 Fax: (301) 480-0855 -----Original Message----- From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu] Sent: Wednesday, March 10, 2004 5:23 PM To: Stiles, David (NIH/NIDDK) Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Problems with Hu6800 and GCRMA... On Wed, Mar 10, 2004 at 03:36:02PM -0500, Stiles, David (NIH/NIDDK) wrote: > Dear Bioconductor Mailing List, > > I'm currently trying to run GCRMA on some Hu6800 Affymetrix GeneChip > data and keep receiving the following error after I type "eset > <-gcrma(Data)": "Please download and install the hu6800probe library from: > http://www.bioconductor.org/data/metaData.html". I went to the website and > downloaded the probe library file from that webpage but I'm still receiving > the error message. I have download other probe library files for other old I think the problem might be due to naming conventions. Somehow the annotation package and cdf packages are called hu6800 but the probe package is called hugeneflprobe - I suspect we need to rename it. Does anyone know in Biocore know if there is a good reason for this naming convention? In most cases you are better off using the internal to R mechanisms for downloading data packages etc. Those include the functions available through the Packages menu on Windows and install.packages2 in the reposTools package from Bioconductor. So something like library(reposTools) install.packages2("pkgnamehere") should work...but in this case it doesn't since hu6800probe does not exist. > Affymetrix GeneChip designs and they have worked fine except for Hu35KD > which I can't download from the Metadata webpage because the link is bad. > Could you great guys and gals at Bioconductor fix the link for the Hu35KD > probe library file and find a solution for current problem I'm having > between GCRMA and Hu6800 probe library file? Thank you for your time on > this matter. > Yep, we're going to fix it - thanks for the report. And we will send you a properly named version of the 6800 probe package if you would be so kind as to tell us your OS (I'm guessing Windows since that was the broken link....) Robert > David Stiles > Technologist > NIH/NIDDK Microarray Core Facility > Phone: (301) 496-0175 > Fax: (301) 480-0855? > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------ + | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------ +