Hello, I loaded a few CEL file from MOE430A experiments. Strangely, many PM values are negative! As a result, RMA and other routines did not work. Any ideas?? See scripts below. I am puzzled! I am running Bioconductor 1.6, R 2.1.0, with moe430acdf loaded. Thanks! Simon ################################################################ > result.batch<- ReadAffy(filenames=CEL.fileNames) > result.batch AffyBatch object size of arrays=712x712 features (11886 kb) cdf=MOE430A (22690 affyids) number of samples=3 number of genes=22690 annotation=moe430a > > x<-pm (result.batch) > dim (x) [1] 249958 3 > x[1:10,] P3-real.CEL P4-real.CEL P5-real.CEL [1,] 1.001874e-23 -2.117582e-22 4.567573e-08 [2,] 1.603000e+03 1.240000e+03 2.319708e-39 [3,] -8.589935e+09 1.454000e+02 2.759000e+03 [4,] 3.503246e-44 8.100000e+01 4.539706e-08 [5,] 5.238000e+02 4.010000e+02 2.319436e-39 > result.degradation<- AffyRNAdeg(result.batch) Error in var(x, na.rm = na.rm) : missing observations in cov/cor In addition: There were 50 or more warnings (use warnings() to see the first 50) > > MAplot (result.batch) Error in rowQ(imat, half) : cannot handle missing values -- yet In addition: Warning message: NaNs produced in: log(x, base)