[BioC] RMA and GeneSpring?

Fátima Núñez fnunez at usal.es
Mon Oct 6 20:45:52 MEST 2003

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of Dapeng Cui
> Sent: 06 October 2003 19:30
> To: <
> Subject: [BioC] RMA and GeneSpring?
> I'm new in Bioinfor and never used Bioconductor before.The question
> are too naive but i really want the answer. My work is to compare
> cell types with affy chips and I already got some preliminary raw
data. My
> plan is to normalize the data using RMA then analyze using GeneSpring,
> not familiar with either one though. Someone told me the software
> RMAExpress is enough if I don't want other functions of BioC. So I
> download and ran the RMAExpress. Then i realized that GeneSpring only
> takes linear values and the results from RMAExpress look like in log
> value. So i have two questions:
> 1) If i transform the RMA data to linear value for GeneSpring, are
> base 2?

Yes, they are.

> 2) GeneSpring needs the data to be normalized around 1 (median). 

Not necessarily. GeneSpring recommends to do that normalization, but you
can modify the normalization steps to suit your pourposes.

But i
> don't want to do any other normalization except RMA. So can I work
> these RMA data (transformed to linear, obviously the median is not 1 )
> GeneSpring? 

Yes, you can. All you have to do is to remove all normalization steps
that appear by default in the GeneSpring corresponding window and ignore
their warnings ;-)

Or, how should I combine RMA and GeneSpring anyway? Thank you
> for your help.

> dapeng
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