S Peri wrote: > Hi, > I am also trying to parse CDF files to get the > coordinates of the porbesets and their names. The > reason I need to get is that, I want a reference for > each probeset on the chip in this case postion on the > chip. This allows my to query specifically some > probesets depending on the position. I know this > might sound too much, however, I am interested in > implementing this in the db schema I have. > > I tried Laurent's suggestions. It worked for one > probeset. By induction, it should then work for all probesets. (and since apparently you want to store everything in a database, I do not see the problem...) > Is there any command where I get an object > with all probesetIDs and their coordinates written > adjascent to probeset coordinats. Follow the second suggestion and make an instance of class Cdf (see package 'makecdfenv'). Then: i <- seq(along=c(mycdf@names)) cbind(mycdf@names.levels[mycdf@names], indices2xy(i, nr=nrow(mycdf@names)) ## ...this is untested... you may still have to read the ## documentation... > Thanks. > Peri. > > > --- Laurent Gautier <lgautier@altern.org> wrote: > > >>Srinivas Iyyer wrote: >> >>>Hi, >>> >>>CellHeader=X Y MEAN STDV NPIXELS >>> 0 0 152.0 30.0 25 >>> 1 0 5024.5 475.3 20 >>> 2 0 151.0 25.0 25 >>> 3 0 5017.0 558.9 25 >>> 4 0 205.5 71.5 20 >>> >>> >>> >>> >>> >>>How can I get to know what 0 0 , 1 0, 2 0 >> >>correspond >> >>>to 1001_at or XXXX_at. Can some one please help. >> >>I >> >>>want to get the spot and the corresponding probe. >> >>The information is contained in the relevant CDF >>file. >> >>Did you consider using the 'affy' package ? >> >>The help page for the function 'xy2indices' might be >>worth a look. >> >>However, if you want to go from XY coordinates to >>probe set names often >>in your code, the most efficient >>would be to use the class Cdf (now found in the >>package 'makecdfenv'). >> >> >>L. >> >> >> >>>Thank you. >>> >>>Srini >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >