[BioC] How to search for coexpression?

[michael watson (IAH-C)]

OK, so your data can be accessed as a data.frame by executing:
 
library(Biobase)
exprs(eset)
 
The function cor computes an all against all correlation matrix, but depending on the size of your data set, this may cause a few problems with memory, I don't know.
 
If you do use cor, you will have to transpose your data first as cor computes correlation coefficients on columns, not rows.  
 
?cor
?t
 
You may also need
?as.matrix
 
If you need to convert a data.frame to a matrix

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of stueber at mpiz-koeln.mpg.de
Sent: Tue 07/03/2006 11:09 AM
To: bioconductor at stat.math.ethz.ch
Cc: stueber at mpiz-koeln.mpg.de
Subject: [BioC] How to search for coexpression?



Dear colleaques,

After reading data from affymetrix CEL files I would like to
get information about coexpressed and non-coexpressed genes for
a chosed set of probesets.

I start with:

>library(affy)
>Data <- ReadAffy()
>eset <- rma(Data)

This give me a big array of all intensities for
all probesets and experiments.
But what to do then?

Any hints appreciated.

Kurt Stueber

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