GCP Microarray analysis

 

For the analysis of data from microarray experiments the GCP developed and/ or adapted several software facilities. These were introduced at 2007 and 2009 GPC organized workshops. The manuals and bioinformatics tools and scripts are available from the Cropforge microarray data analysis website (http://cropforge.org/frs/?group_id=73 )

The GCP microarray (MA) data analysis system, in its current state, is a collection of software tools, either developed in-house or 3rd party tools extended/adapted to use GCP data. A quick use tour will be showing its use for the following case study.

• Significance analyses : statistical determination of differentially expressed genes between treatments / genotypes / T x G, etc.. 


• Gene expression profile clustering


• Genome-position dependent region of correlated expression (RCE) analysis


• Genome-position dependent aggregation of Differentially Expressed Genes (DEG) analysis


• Enrichment (over-representation) analysis 

All software/ scripts and their complete documentation can be found in the Cropforge microarray data analysis website (http://cropforge.org/frs/?group_id=73 ). 

For a quick overview of the microarray analysis tools and their functions read http://cropforge.org/frs/download.php/373/GCP_Microarray_Analysis_Cookbook.pdf

Tutorials for the GCP Microarray Analysis System are provided here and here.

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