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