Dear Dr. Janssens, In the studies we did using custom Agilent arrays, the intraspot correlation is about 0.3. The intraspot correlation is residual correlation, so it is adjusted for the mean. This makes it much lower then the correlation between the channels that you might compute naively. Naomi At 07:04 AM 6/5/2009, you wrote: >Dear Dr. Altman, > >on the BioC forum I have noticed you are an expert and frequent user >of the anaysis of indivdual channel data of minro-arrays. >I am struggling already for a couple of weeks with a very low >(alomost zero) consenus intraspotcorrelation in limma. I am afraid >that this affects the testing procedure. I read on the forum that it >should approach one. >I am using custom made 8x15k agilent arrays in an interwoven loop >design without reference. > >Do you know what can be the reason for my low intraspotcorrelations? > >thank you and kind regards, > >Thierry Janssens > >-- >Thierry K.S. Janssens >Vrije Universiteit Amsterdam >Faculty of Earth and Life Sciences >Institute of Ecological Science >Department of Animal Ecology, >De Boelelaan 1085 >1081 HV AMSTERDAM, The Netherlands >Phone: +31 (0)20-5989147 >Fax: +31 (0)20-5987123 >thierry.janssens at ecology.falw.vu.nl > > Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111