hi,

i am trying to analyze Affymetrix Promoter tiling arrays with R, but have
not found a way to do this so far. first of all i want to import the CEL
files, and to get the mapping between the probes and the genomic locations.
reading the cel files is per se not so difficult, since the affxparser and
oligo packages provide functions for that, but when it comes to annotate the
probes i have difficulties. i generated a platformDesign object/package with
the makePlatformDesign package (makePDPackage, version 1.2.0, supplied the
bpmap file, and as parameter file1 the CIF file).
so far i got no problems, but now i do not know how to handle the data i
read in (since there is also a lot of documentation missing for the oligo
package).
how can i combine the information from the platformDesign object with the
read CEL files? in the platformDesign there is the information of the
chromosomal location of the probes, but i suppose that the ordering of the
probes in the platformDesign object differs from the read CEL files
(TilingFeatureSet class). i also checked all slots from the platformDesign
object, but the slot "indexes" is an empty list. the environment stored in
the "featureInfo" slot contains a "order_index", but there is no description
about that, so i don not know if i should use this to reorder the elelments
from the platformDesign, or the ordering of the elements in the
TilingFeatureSet.
can anyone please help here, or is there an other way to read Affymetrix
tiling array data (and to combine the data with the probe annotation)?

thanks in advance, jo

-- 
Johannes Rainer, PhD
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 33
Email: johannes.rainer@tcri.at
           johannes.rainer@i-med.ac.at

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