well two ideas then: - big endian / little endian problem (can you detail the architecture your are running on ?) - entanglements with the new features of R to read multibytes charsets. (were your CEL files generated/edited on a machine with 'exotic' locales ?) > 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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >