Re: Analysis of Microarray Data using ASReml

From: Bruce Southey <southey_at_UIUC.EDU>
Date: Tue, 7 Sep 2004 09:48:27 -0500

What is your platform (OS and installed memory)?
You may have insufficient memory available.

You can avoid your first model by subtracting the means of the each dye channel
for each slide.

For your second question, either create seperate datasets (easy with a scripting
language) or use the DIAG structure in a full model so that each gene gets
seperate residual and slide variances. The latter case will probably mean lack
of memory.

Using Maanova with R is probably a better solution than using Asreml for this
since you have access to various transformations and other tools.


---- Original message ----
>Date: Tue, 7 Sep 2004 10:03:53 -0400
>From: Fikret Isik <fisik_at_UNITY.NCSU.EDU>
>Subject: Analysis of Microarray Data using ASReml
>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 - 09:48:27 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)