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Topic: question regarding celintensityread in bioinformatics toolbox
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James

Posts: 77
Registered: 10/24/05
question regarding celintensityread in bioinformatics toolbox
Posted: Dec 6, 2011 4:00 PM
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Hi,

I am using celintensity read to read some microarray data (gene 1.0 ST platform from affy). One question is that after reading the cel files, one of the field "probeIndices" only contains a bunch of number in series from 0 to N-1, where N is the total number of probes within a probe set. It does not return anything like the probe ID (not probe set ID), probe sequence, or the x,y of the probes. The question is when I compare with the probe sequence file on affy website, how can I know whether the order of the probes within the same probe set are read from celintensityread function are the same as the order in the probe sequence file? To be more specific, one transcript cluster ID: 7957417, it contains 28 probes. from the one read from function celintensity, you only know the probe indices are from 0 to 27, but there is no way to know other things like probe ID (not probe set ID), probe
sequence, etc.

Thanks,

-James



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