How to create a custom CDF ?
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@alexander-stoddard-833
Last seen 10.2 years ago
Greetings all, I am interested in using the gcrma method to analyze a set of data that extends over the mgu74av1 and mgu74av2 Affy chips. I suppose my best bet is to create a custom CDF environment and Probe package which contain only the common probesets across the two versions. Does this seem reasonable? I can think of two ways to approach this: 1) create custom files representing the Affy CDF and probe files (this I believe I can do). Then use tools in Bioconductor to create the R packages. I guess those include makecdfenv (with which I am not familiar) and whatever is needed to create the probe data. 2) work with R to extract the common data from the existing packages into new ones. I would welcome advice on which would be easier plus some pointers on what I need to do in R to achieve either one. If I am successful would such a combined mgu74av1 and mgu74av2 CDF environment be of sufficient interest to others to make generally available? Many thanks, Alex Stoddard
mgu74av2 cdf probe affy makecdfenv gcrma mgu74av2 cdf probe affy makecdfenv gcrma • 1.2k views
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.2 years ago
There is such a CDF package for mgu74a and mgu74av2 at http://www.stat.berkeley.edu/~bolstad/mixtureCDF/MixtureCDF.html Ben On Wed, 2004-06-30 at 11:55, Alexander Stoddard wrote: > Greetings all, > > I am interested in using the gcrma method to analyze a set of data that > extends over the mgu74av1 and mgu74av2 Affy chips. > > I suppose my best bet is to create a custom CDF environment and Probe > package which contain only the common probesets across the two versions. > Does this seem reasonable? > > I can think of two ways to approach this: > 1) create custom files representing the Affy CDF and probe files (this I > believe I can do). Then use tools in Bioconductor to create the R > packages. I guess those include makecdfenv (with which I am not > familiar) and whatever is needed to create the probe data. > > 2) work with R to extract the common data from the existing packages > into new ones. > > I would welcome advice on which would be easier plus some pointers on > what I need to do in R to achieve either one. > > If I am successful would such a combined mgu74av1 and mgu74av2 CDF > environment be of sufficient interest to others to make > generally available? > > Many thanks, > > Alex Stoddard > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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