Question: affy Yeast 2.0 annotation
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gravatar for Jacob Michaelson
14.7 years ago by
Jacob Michaelson320 wrote:
I'm having difficulty finding a reasonable way to format the annotation data that Affymetrix provides (both MAGE-ML XML and a similar CSV file) into a BioC annotation package. I've read the AnnBuilder vignette and it seems to assume that one starts with a format other than what Affy provides. I've also read that the RMAGE-ML package can take the Affy MAGE-ML package and format it for use within limma, and a few other packages, but affy (or annaffy or AnnBuilder) isn't listed as one of them. Can anyone help me out as to what method would be most efficient for formatting this MAGE-ML file into a format acceptable for use within BioC as a general annotation file? I can't find any such packages currently available for the Yeast 2.0 chip. Thanks in advance, Jake Michaelson
ADD COMMENTlink modified 14.7 years ago by Vincent J. Carey, Jr.6.3k • written 14.7 years ago by Jacob Michaelson320
Answer: affy Yeast 2.0 annotation
0
gravatar for Vincent J. Carey, Jr.
14.7 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
> I'm having difficulty finding a reasonable way to format the annotation > data that Affymetrix provides (both MAGE-ML XML and a similar CSV file) > into a BioC annotation package. > > I've read the AnnBuilder vignette and it seems to assume that one > starts with a format other than what Affy provides. I've also read > that the RMAGE-ML package can take the Affy MAGE-ML package and format > it for use within limma, and a few other packages, but affy (or annaffy > or AnnBuilder) isn't listed as one of them. RMAGEML is currently devoted to conversion from MAGE-ML archives of experiment results to marray type data structures in R. I understand that this functionality will be expanded in the direction of affy archives, but I am not sure it will address the use of MAGE-ML for creation of platform annotation environments. > > Can anyone help me out as to what method would be most efficient for > formatting this MAGE-ML file into a format acceptable for use within > BioC as a general annotation file? I can't find any such packages > currently available for the Yeast 2.0 chip. I will look at the MAGE-ML serialization and see if it is easy to come up with something using the XML library. But it may well be easier to work from the CSV. AnnBuilder would clearly be the tool of choice for this activity, but I don't believe it can transform directly from an Affx annot CSV to the desired set of environments. We can improvise something fairly simply; I recently did it for zebrafish, but the results do not emulate exactly the structures in the other affy chip annotation packages. I will post some partial solutions in a few moments. There are various ways of getting something useful, and the path taken will depend upon the ultimate requirements. If we want to be sure that something like annaffy will behave well with the target platform, we may have more stringent requirements than if we are just interested in doing manual lookups.
ADD COMMENTlink written 14.7 years ago by Vincent J. Carey, Jr.6.3k
What is the current level of support in Bioconductor for the binary Affy GCOS formats? Is there a current best practice for converting from TEXT to BINARY and vice versa? [ Sorry if this is a repeat question, I got the mail dumps for last few months and greped around in it but could find little ]
ADD REPLYlink written 14.7 years ago by Richard Finney180
Richard Finney wrote: > What is the current level of support in Bioconductor > for the binary Affy GCOS formats? Currently the binary .cel files are supported. Support for binary .cdf files should exist very soon. For the average end user, the binary .cdf support should be a moot point, as the affy package automagically downloads and installs required cdfenvs. All but five or six of the existing .cdf files are downloadable from the BioC website, and as soon as we have support for the binary .cdfs they will all be available. > > Is there a current best practice for converting from > TEXT to BINARY and vice versa? > > [ Sorry if this is a repeat question, I got the mail > dumps for last few months and greped around in it but > could find little ] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
ADD REPLYlink written 14.7 years ago by James W. MacDonald51k
I have created a custom CDF file. The purpose is to measure the expression of splice variations. I place the file in the same directory as the CEL files and crank up R and do the usual BIOC incantation. Based on a suggestion offered by the brainiacs at University of Michigan ( http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf readme.htm#How_to_use_the_custom_CDF_file:_ ) I try something like this ... data<-ReadAffy(); data@cdfName<-"NEW.CDF" But subsequent data processing calls attempt to connect to the internet and get a CDF file from there. Obviously, I missing something. Anybody got any ideas? Please add to any "RTFM" responses a specific FM to read. Thanks! Rich
ADD REPLYlink written 14.7 years ago by Richard Finney180
I think that you need to hand edit the cel files and put the name of your new custom CDF env in there. Since that is where the software looks to decide what CDF it needs. Robert On Jan 25, 2005, at 8:04 PM, Richard Finney wrote: > > I have created a custom CDF file. > > The purpose is to measure the expression of splice > variations. > > I place the file in the same directory as the CEL > files and crank up R and do the usual BIOC > incantation. > > Based on a suggestion offered by the brainiacs at > University of Michigan ( > http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/ > cdfreadme.htm#How_to_use_the_custom_CDF_file:_ > ) > I try something like this ... > > data<-ReadAffy(); > data@cdfName<-"NEW.CDF" > > But subsequent data processing calls attempt to > connect to the internet and get a CDF file from there. > > Obviously, I missing something. > > Anybody got any ideas? > > Please add to any "RTFM" responses a specific FM to > read. > > Thanks! > > Rich > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+
ADD REPLYlink written 14.7 years ago by rgentleman5.5k
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