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

[Mark Cowley]

Hi Martin,
in my experience comparing GeneSpring to R/Bioc values, even for a  
simple RMA produces slight differences.
Just what GeneSpring actually does to the data is a bit of a black  
box. Perhaps a question to the genespring users group (genespringusers at yahoogroups.com 
) might yield a better answer.

I'd also suggest using log2 before taking all of the normalizations to  
medians, since this might account for some small differences.
i'm not familiar with the "median shift to percentile of 75", so  
perhaps someone else can help with that.

cheers,
Mark
On 16/06/2008, at 6:48 PM, olszewski at atlas-biolabs.de wrote:

> 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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