Creating Custom CDF
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naresh kumar ▴ 40
@naresh-kumar-3577
Last seen 9.5 years ago
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. 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]]
cdf makecdfenv cdf makecdfenv • 1.3k views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States
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 > 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-5106
Last seen 11 hours ago
United States
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 > > > -------------------------------------------------------------------- ---- > Love Cricket? Check out live scores, photos, video highlights and more. > Click here > <http: in.rd.yahoo.com="" tagline_cricket_2="" *http:="" cricket.yahoo.com="">. -- 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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