[Bioperl-l] Microarray ANOVA module

[Robinson, Peter]

Hi All,

I would like to ask about the status of Bioperl's plans for modules for microarray data analysis. I have written a module that does ANOVA (F test) analysis of microarray data and would like to make it accessible somewhere but am not sure about the proper place and would like to ask if someone on this list would be willing to take a look at it.

The module can be used to analyze groups of repeats of experiments (such as a time course), taking the Stanford .pcl format as input and outputting in the GeneCluster format. Only genes that pass the significance test are output. I am planning on extending the module to include other functions such as T test or fold change filters as well as XML/format interconversion.

The module depends on Statistics::Distributions and uses some of the statistics functions from the Perl algorithms book.

To use it:

use ArrayANOVA; (Not a nice name...)

my $anova = new ArrayANOVA(
	filename => "inputfile.txt",
	outputfilename => "outputfile.txt",
	significance_level => "0.01",
	groups => [
		[4,5,6,7],
		[8,9,10],
		[11,12,13,14],
		[15,16,17],
		[18,19,20],
		[21,22,23],
		[24,25,26,27]
		],
	replace_missing => "1"
	);

$anova->filter_significant_genes();
$anova->outputGeneClusterFormat();

best,

Peter

Dr. med. Peter Robinson
Institut für Medizinische Genetik
Universitätsklinikum Charité
Augustenburger Platz 1
13353 Berlin
Germany