Hi, I am using limma for the first time and have a dataset that has some negative values once the background has been subtracted from the spots. These are in duplicate so I am using the dupcor.series method. This works ok until I try and add in the backgroundCorrect method=minimum and then I get the following error: Error in array(val[["varBeta"]], c(rnkm1, rnkm1), list(namCoef, namCoef)) : length of dimnames[1] not equal to array extent Firstly will it make any difference to the order of my differentially expressed genes to perform some type of background correction, if so what does the error message mean? and secondly what kind of values in the top table am I looking for? The highest B value I have is -0.6 (without any background correction) which seems really low - is this any good? Any help is appreciated, Helen ----- Helen Cattan <helen.cattan@jenner.ac.uk> Bioinformatics The Edward Jenner Institute for Vaccine Research Compton, Newbury, Berkshire, RG20 7NN UK Tel +44 (0)1635 577968 / Fax +44 (0)1635 577908 [[alternative HTML version deleted]]