Preprocessing of RSV Gene Expression Profiles for DARPA Project
   															Hero Group
   									Graduate Program in Bioinformatics
   							Electrical Engineering and Computer Science
   												University of Michigan
   														 Aut 31, 2008
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

   
1.	Preprocessing method
=====================================
		Expression intensities are computed from CEL files using Michigan custom chip definition 
		file (CCDF) version 10. This CCDF is based on human genome Build 36, Version 2, Sep 14, 2006
		by National Center for Biotechnology Information (NCBI). The following parameters are used 
		when computing probeset level expression measures:
		
		* Background correction: Robust Multichip Average (RMA) convolution
		* Normalization: Quantile normalization
		* Summarization: Median polish
		
		More details please see:
		Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget 
		Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data 
		Nucleic Acids Research 31(4):e15
		
		Note the intensity values are in Log base 2 scale.


		
2.  Summary of samples
=====================================
		Total number of arrays:					164



3. Quality assessment
=====================================
		The residual plots show excellent data quality with only 8 chips having minor to mild artifacts.
		(see attached PowerPoint).



4. Files
=====================================		
	1) darpa.rsv.rma.(164).ccdf.txt
		 RMA preprocessed singal intensity for complete set of 164 gene expression profiles.
		 
	2) residual.plots.zip
		 Archive file including all the residual plots for visual examination.
		 
	3) darpa.rsv.rma.(164).residual.ppt
		 Slides showing chips with minor to mild artifacts.
		 
  4) darpa.rsv.key.txt
     Key mapping chips, samples and subjects.

	
	
5. Others		
=====================================
If you have any question regarding this dataset, please email Prof Alfred Hero at 'hero@umich.edu' 
or Yongsheng Huang at 'huangys@umich.edu'.