Analysis of Microarray Data using ASReml

From: Fikret Isik <fisik_at_UNITY.NCSU.EDU>
Date: Tue, 7 Sep 2004 10:03:53 -0400

Hi ASReml Users,

I am working on a gene expression (microarray) data set of 398000
observations. I fitted the following mixed model to normalize data.
log2i ~ mu dye !r slide slide*dye
The model it self is not complicated, but ASReml failed to finish the
analysis. I increased the memory allocation 3 fold (-S3). That did not
help either. I received the following error message: "Severe <157>,
Program Exception-access violation". Is there a way to overcome this
problem? Can ASReml handle this kind of large data sets?'.

My second questions is about fitting a gene-by-gene model using the
normalized data. In SAS this can be done using the 'BY' statement before
the model statements as follows.

proc mixed data=&ds cl lognote;
 BY geneid ;
     class dye slide sample;
     model log2in=dye sample/outp=array.gene_res ;
     random slide;

SAS runs the model for each gene separately. However, in general, if the
data are large, the log message window overflows and it takes quite a
long time to finish the job. Is there a way to fit the same model in
ASReml for multiple genes each time for a different gene and to automate
the job? Any comments will be appreciated.

Fikret Isik

Fikret Isik, Research Assistant Professor
North Carolina State University
Department of Forestry,
Campus Box 8002, Raleigh, NC 27695, USA
Phone 919-515-5029, Fax 919-515-3169
Received on Tue Sep 07 2004 - 10:03:53 EST

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