PoGO For POSOC README
29 September 2006
Ian C. Grieve

PoGO consists of:
-> PoGO.pl: Pipeline script to carry out the PoGO statistical analysis of differential expression Affymetrix datasets.
-> PoGO_config.txt: Configuration file for PoGO, in which the input files and parameters are specified.
-> PoGO Modules: Statistics::FET - Fisher's Exact Test module by tlm (PerlMonks), adapted for PoGO; Modules::ClusterFisher (Fisher's Exact Test implementation subroutines); Modules::PermutationTests (Permutation Testing implementation subroutines); Modules::BenjaminiHochberg (Benjamini-Hochberg Multiple Testing Correction implementation subroutines).

PoGO requires:
-> Perl installation.
-> POSOC, or a suitable POSOC clustering output file. POSOC requires Java and the Java OpenJGraph library.
-> CPAN Modules: Math::Pari (required by the Fisher's Exact Test module), List::Util (required for permutation testing).

PoGO optional component:
-> Affyfile Converter perl script - to convert NetAffx CSV annotation file to MTX2 format suitable for POSOC.


How to use PoGO:

1. Configure PoGO by editing the PoGO config file in a text editor. Specify the names of the input files, and the PoGO parameters as follows:

INPUT FILES:
MTX2: The name of the MTX2 file that was used by POSOC to generate the clusters. This should be distilled from the CSV file obtained from the Affymetrix website (NetAffx resource) using affyfile_converter.pl if not already present.
FULL: The full list of probesets (in the form of Affymetrix IDs, one per line) on the chip.
DE: The list of probesets considered to be differentially expressed or otherwise of interest for comparison against the baseline (again, in the form of Affymetrix IDs, one per line).
CLUSTERS: The clustering output produced by POSOC.

PARAMETERS:
FISHER_MIN: The minimum number of DE genes annotated to a cluster for it to be included in Fisher's testing and in the Benjamini-Hochberg multiple testing correction. This should be an integer. Default 0.
PERMS: Number of permutations to be carried out in permutation testing. This should be an integer. Default 1000.
BH_SIG: Benjamini-Hochberg significance threshold. Default 0.1 (10%). 

All of the input files must be in the same directory as PoGO when PoGO is run.


2. Run the PoGO script to commence the pipeline of analysis.

3. The output of the statistical tests, tab-delimited, will be written to PoGO_results.txt.
