> > >Hello > >There are approximately 6000 different genes on the arrays, there are two spots for each gene >The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: > > Min. 1st Qu. Median Mean 3rd Qu. Max. > 4.00 32.00 71.00 86.59 135.00 244.00 > >(Distance here means number of spots between the two duplicates) > >The function duplicateCorrelation in limma can be used to estimate correlation between within-array duplicates, the methodology is based on the assumption that duplicates are equally spaced. Since this assumption is not fulfilled here does this means that I cannot calculate the correlations and must take the average of the duplicates? Are there some functions to do this in limma or other BioC packages > Hi ingunn & all I could be wrong about this but can you get round this in limma by: normalising the data first(to allow for the physical location on the array) followed by re-arranging the normalised data so that duplicate genes appear next to each other and therefore have equal spacing ? I.e spacing of 1 or similar. You obviously have to make new genelists for the "rearranged" order but I can't see any obvious problems with further analysis such as the linear model fitting etc. If you only have two replicates then it should be ok...... I do this routinely but the limma authors might be able to suggest a better alternative ? Jason >-- >-------------------------------- >Jason Skelton >Pathogen Microarrays >Wellcome Trust Sanger Institute >Hinxton >Cambridge >CB10 1SA > >Tel +44(0)1223 834244 Ext 7123 >Fax +44(0)1223 494919 >-------------------------------- > >