Hello everyone, I have two replicate chips and one of them suffers with some compact defects on it. I was trying to use the package Harshlight to correct for these errors and getting an error message which I am unable to get rid of. While the following command works(replacing erroneous values with NA) --- > test<-Harshlight(data_aha[,1],na.sub=TRUE,report.name="test.ps") The following command (trying to replace with the other chips' median value) does not work --- >test<-Harshlight(data_aha,report.name="test.ps") and gives the following error --- Error in apply(int.subs[is.na(result), -i], 1, median) : dim(X) must have a positive length Here is my sessionInfo -- R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] C attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] ath1121501cdf_2.6.0 Harshlight_1.18.0 altcdfenvs_2.10.0 hypergraph_1.20.0 [5] graph_1.28.0 makecdfenv_1.26.0 matchprobes_1.20.0 Biostrings_2.16.9 [9] IRanges_1.6.17 AnnotationDbi_1.10.2 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 KernSmooth_2.23-3 RSQLite_0.9-2 affyio_1.16.0 [5] preprocessCore_1.10.0 Many thanks for your help. vas [[alternative HTML version deleted]]