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
> >
> >
> >
> >
> >
> >
> > Looking for local information? Find it on Yahoo! Local
>
http://in.local.yahoo.com/
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> </mc>
> >
https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> -- 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
