[BioC] How to calculate the values lige GeneSpring from the raw intensities (Agilent)

[olszewski at atlas-biolabs.de]

Hello,

we use one-color Agilent chips (4x44 whole human genome) and I try to
calculate the intensities like GeneSpring does. The problem is, that my
values are a little bit different and i don't know why.

First I read in the data from the Agilent-Files "gProcessedSignal".
Some genes are nor unique, so I take the mean value for these gene
intensities.
Like GeneSpring I first divide each raw intensity value by the median of
the chip and then divide each value by te median of each gene.
Now I have the normalized values and I use the log2 function to recieve
similar values to the GeneSpring values, but here is a little variation
and the only thing I hav found, what GeneSpring does is the "median shift
to percentile of 75". How can I perform this median shift to percentile?
Maybe this is the key to find the correct values?

Thanks in advance for any help!

Martin


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