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
>>
>>**********************************************
>>
>>
>>
>>This email message may contain legally privileged and/or
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>>
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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
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
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> This email message may contain legally privileged and/or
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University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
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