[BioC] [limma] Separate Channel Analysis of 2 color data with summarization

[Ana Conesa]

Dear List,

I am analyzing some yeast Nimblegen arrays following the separate channel 
analysis of 2 color data of the limma package. After within and between 
arrays normalization steps I did a summarization (medianpolish of M and A 
values for 12 spots/gene) step to reduce the number of features for 
differential expression analysis. My idea was then to calculate 
intraspotcorrelation and use the lmscFit function. My question is whether it 
should be OK to compute the intra spot correlation and the linear model using 
these summarized values. One  result that calls my attention is that the 
intraspotcorrelation computed on the summarized values has a consensus value 
of 0.517.  From other posts in the list, it has been mentioned that intraspot 
correlation should be above 0.8, so I am wondering if this approach is 
conceptually correct.

Thanks for any suggestion on this topic

Regards

-- 
Ana Conesa
Bioinformatics and Genomics Department
Centro de Investigaciones Principe Felipe
Avda. Autopista Saler 16,
46012 Valencia, Spain
Phone: +34 96 328 96 80
Fax:   +34 96 328 97 01
http://bioinfo.cipf.es/aconesa
http://www.blast2go.org