[BioC] Custom CDFs from U mich for GeneChip Analysis

[James W. MacDonald]

Hi Ken,

Lo, Ken wrote:
> Hi Jim,
> 
> When I tried what you suggested, this happened.
> 
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encount
> ered:
> Specified environment does not contain hs133phsrefseqsnp6cdf
> Library - package hs133phsrefseqsnp6cdf not installed
> Data for package affy did not contain hs133phsrefseqsnp6cdf
> Bioconductor - hs133phsrefseqsnp6cdf not available
> 
> Do I have to use a data at cdf <- "hs133phsrefseqsnp6cdf"?

Please don't take a list exchange off-list. We consider the list 
archives a useful resource, but it will only remain so if 
questions/answers are actually made via the list.

As to your question, what I told you to do was accurate, and you don't 
need to do any more or less. However, you do have to use the name of a 
package that we distribute (and that isn't one). You can look at the 
listing of available MBNI chips using the biocViews page:

http://www.bioconductor.org/packages/1.9/MBNICustomCDF.html

which is just MBNI packages regardless of species, or

http://www.bioconductor.org/packages/1.9/Homo_sapiens.html

which is human chips regardless of manufacturer/MBNI.

If you want to use that particular chip, which is now two versions old 
(they are on version 8), you can go to the mbni website and 
download/install by hand

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v6.asp


Best,

Jim

> 
> Best regards,
> 
> Ken
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: Friday, October 06, 2006 4:50 PM
> To: Lo, Ken
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Custom CDFs from U mich for GeneChip Analysis
> 
> Hi Ken,
> 
> Lo, Ken wrote:
> 
>>Hi all,
>>
>>I just recently came across a paper by Dai et al, Nucleic Acids 
>>Research, 2005 that talks about transcript definitions of the GeneChip
> 
> 
>>arrays being based on old genome builds.  They have in turn 
>>reannotated the platforms based on specific critieria outlined in the 
>>paper.  Has anyone tried their custom CDFs?  Also, how would one patch
> 
> 
>>this to use with gcrma?
> 
> 
> No patch needed. These packages are all available from BioC. There is a
> cdfname argument for all of the functions you might need to use to do an
> analysis that will cause an automatic download and installation of the
> correct package(s).
> 
> The package names are a bit cryptic, mainly because they need to
> indicate the species/chip/species used for annotation/database, so for
> instance the annotation package for the HG-U133plus2 chip (annotated to
> Entrez Gene) would have a name like hs133phsentrezg.
> 
> You could use these chips like this:
> 
> dat <- ReadAffy(cdfname="hs133phsentrezgcdf")
> eset <- rma(dat)
> gset <- gcrma(dat)
> 
> Best,
> 
> Jim
> 
> 
> 
>>Best regards,
>>
>>Ken
>> 
>>
>>**********************************************
>>
>>Ken Lo, PhD
>>Post-Doctorate Fellow
>>Department of Cancer Genetics
>>Center for Genetics and Pharmacology
>>Roswell Park Cancer Institute
>>Elm and Carlton Streets
>>Buffalo, New York 14263
>>Telephone:  716-845-3941
>>Fax:         716-845-3940
>>E-mail:      Ken.Lo at RoswellPark.org
>>Web:        www.RoswellPark.org <http://www.roswellpark.org/>  
>> 
>>Located in the
>>Buffalo Life Science Complex
>>on the Buffalo Niagara Medical Campus
>>
>>**********************************************
>>
>>
>>
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> 
> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> 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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> This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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