this is what you have to do. in the exprs (intensity) slot of an AffyBatch put a matrix with as many columns as arrays and as many row as number of probes on the array. in each column put the vector of intensities of each array. a row must represent a unique location on the array. no you need to create a hash table enviromnet with varialbles with names of the probesets. the variabes need to be 2-column matrix where the first column has the positions of the PMs of that probe set and the second row the MMs. for example the variable 1000_at could be 1 641 2 642 12 652 etc.. now in the cdfName slot of the exprset put the name of this enviromnet. this should get you on your way. look at the example data(Dilution) to get a better idea. you will that the environment (loaded through a library) hgu95av2cdf has the variables 1000_at, 1001_at, etc... with the positions. hope this helps, -r On Tue, 4 Feb 2003, Tibor van Rooij wrote: > Hi! I would very much like to use the MBEI method, however all my data is stored in a database. I can easily access data such as probename x,y positions, pm value mm value etcetera. In the previous version of "affy" I could access slotnames of the objects such as names to put my names into and pm to put my pm values in and get the sytem to calculate the normalization ( so I did not need the original .CEL files) > > I have been looking at the descriptions of the new classes and reading the manual but I cannot find out how to this in this new version. > > Has anybody else attempted this? > > Please let me know. > > Tibor van Rooij > Bioinformatician > McGill University and > Genome Quebec Innovation Centre > 740 Dr. Penfield Avenue, Rm 6212 > Montreal, Quebec H3A 1A4 > Tel: (514) 398-2497 > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

I also remembered to roll in CVS a vignette I had about importing .CEL data from alternative sources. Check the vignette vim.pdf in affy (devel, v.1.1.7) or in the section 'vignettes' of the website (should appear w/ the next automated build). L. On Thu, Feb 06, 2003 at 09:58:15PM -0500, Rafael A. Irizarry wrote: > this is what you have to do. > > in the exprs (intensity) slot of an AffyBatch put a matrix with as many > columns as arrays and as many row as number of probes on the array. > in each column put the vector of intensities of each array. a row must > represent a unique location on the array. no you need to create a hash > table enviromnet with varialbles with names of the probesets. the variabes > need to be 2-column matrix where the first column has the positions of the > PMs of that probe set and the second row the MMs. for example the variable > > 1000_at > could be > > 1 641 > 2 642 > 12 652 > etc.. > > now in the cdfName slot of the exprset put the name of this enviromnet. > this should get you on your way. look at the example > > data(Dilution) > > to get a better idea. you will that the environment (loaded through a > library) hgu95av2cdf has the variables 1000_at, 1001_at, etc... with the > positions. > > > hope this helps, > -r > > > > On Tue, 4 Feb 2003, Tibor van Rooij wrote: > > > Hi! I would very much like to use the MBEI method, however all my data is stored in a database. I can easily access data such as probename x,y positions, pm value mm value etcetera. In the previous version of "affy" I could access slotnames of the objects such as names to put my names into and pm to put my pm values in and get the sytem to calculate the normalization ( so I did not need the original .CEL files) > > > > I have been looking at the descriptions of the new classes and reading the manual but I cannot find out how to this in this new version. > > > > Has anybody else attempted this? > > > > Please let me know. > > > > Tibor van Rooij > > Bioinformatician > > McGill University and > > Genome Quebec Innovation Centre > > 740 Dr. Penfield Avenue, Rm 6212 > > Montreal, Quebec H3A 1A4 > > Tel: (514) 398-2497 > > > > > > [[alternate HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor