[BioC] accessing slots in expresso

Rafael A. Irizarry rafa@jhu.edu
Thu, 06 Feb 2003 21:58:15 -0500 (EST)

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

could be

1 641
2 642
12 652

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


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

hope this helps,

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]]
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