[BioC] How to search for coexpression?

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Mar 7 19:30:23 CET 2006

OK, so your data can be accessed as a data.frame by executing:
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.  
You may also need
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:

>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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