[BioC] Creating Custom CDF

[James W. MacDonald]

Hi Naresh,

Please don't take things off list.

naresh kumar wrote:
> Hello Dr.MacDonald,
> 
> Thank you very much for the Reply,
> 
> I created custom cdf for HG-U133_Plus_2 array by redefining probesets 
> (Assigned new names) .
> I downloaded Oiginal CDF fo this array from affy website.I tried to 
> access a particular probe i'm able to get both PM and MM values but for 
> my customized CDF i'm getting only PM values for a probe but not MM 
> values.So could you please confirm whether this customized CDF does not 
> contain MM values or it a mistake in creating CDF.
> 
> If they is a mistake please suggest me some way to rectify it.
> I created CDF using
> Source : 
> http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch

You may have made a mistake in making your cdf. I can't know because you 
don't show what you did, and the page you point to is for the Affymetrix 
Exon ST chip, so I can guarantee that doesn't reflect what you have done.

If you want help with this, then you should be talking to either 
Elizabeth Purdom directly, or posting on the aroma.affymetrix listserv. 
Posting questions on this list is like going to Apple for help with your 
Windows box that keeps crashing.

If you are just trying to re-map probes to Ensembl Genes, then you can 
use the cdfs that MBNI has been creating for years now, by simply adding 
the argument cdfname = "hgu133plus2hsensgcdf" to your call to ReadAffy. 
See the bottom of this page:

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

for all the available mappings.

Best,

Jim





> 
> Thanks and Regards
> Naresh P
> 
> --- On *Fri, 24/7/09, James W. MacDonald /<jmacdon at med.umich.edu>/* wrote:
> 
> 
>     From: James W. MacDonald <jmacdon at med.umich.edu>
>     Subject: Re: [BioC] Creating Custom CDF
>     To: "naresh kumar" <naresh4836 at yahoo.co.in>
>     Cc: bioconductor at stat.math.ethz.ch
>     Date: Friday, 24 July, 2009, 2:52 AM
> 
>     Hi Naresh,
> 
>     naresh kumar wrote:
>      > Dear mailing list,
>      >
>      > I created custom CDF using
>      >
>      > Source :
>     http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch
>      >
>      > But i got a problem with the created CDF.When trying to access
>     new probesets through makecdfenv package
>      > the pm values are ok but mm values are returning as "NaN".
>      > Please give me some advice how to get mismatch values.
> 
>     Assuming you are using either an Affymetrix Gene ST or Exon ST chip,
>     there are no mm probes, so you can't get any mismatch values.
> 
>     Best,
> 
>     Jim
> 
> 
>      >
>      > Thanks for your help in advance
>      > Naresh
>      >
>      >
>      >
>      >
>      >
>      >
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>     -- James W. MacDonald, M.S.
>     Biostatistician
>     Douglas Lab
>     University of Michigan
>     Department of Human Genetics
>     5912 Buhl
>     1241 E. Catherine St.
>     Ann Arbor MI 48109-5618
>     734-615-7826
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826