[BioC] Problems with Hu6800 and GCRMA...

[Stiles, David (NIH/NIDDK)]

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 at jimmy.harvard.edu] 
Sent: Wednesday, March 10, 2004 5:23 PM
To: Stiles, David (NIH/NIDDK)
Cc: bioconductor at 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 at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

-- 
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| Robert Gentleman                 phone : (617) 632-5250
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| Associate Professor              fax:   (617)  632-2444
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| Department of Biostatistics      office: M1B20
|
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu
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