QCexpression

This Limma-based script visualizes quality of your microarrays. It produces 'per array' plots like MA, Box and density plots.   
Moreover, it produces quality related summary statistics which are plotted for the entire experiment to allow judging
quality in relation to the other microarrays (both in ones own experiment as in a larger set).                      
The script also performs within and between array normalization and exports the data in Stanford format.   

NEW (05/02/2008):
Fixed scales of most plots; allow single channel (RG) output; allow switching of channels including red vs red

NEW (19/02/2008)
Included gene filtering and imputation.
        
Note that we recommend to use Limma also for statistical data analysis; see the Limma manual for instructions.      

The R-scripts, including manual: QCexpression2.1.zip Extract with WinZip and open the manual for instructions.

Additional software for (CGH) micro-array analysis is available from the VUmc microarray core facility.