Dear list, I am getting the error listed below when i try to run the "gage" function within GAGE package: Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I have 1. Gene expression data consisting 4 libraries of "wildtype" and 4 of "knockout", totaling to 8 libraries. Each library contains expression values (normalized) for 6449 genes. 2. Phenotype file contains 2 phenotype classes: "wt" for wildtype and "ko" for knockout. 3. Gene set is custom made gene set. There are a total of 10 genesets containing 1406, 17, 10, 8, 150, 124, 91, 162, 58 and 290 genes respectively. I am able to read all the input files properly. I have done multiple GAGE analysis before but i didn't get error of this kind. Both the Gene set and Expression data are using the same gene ID system. Any help would be really appreciated. Thanks in advance. Thanks, Jung [[alternative HTML version deleted]]

Jung, >From the error message, you get NULL in your gage results (say, your.gage.res) somehow. Type in: your.gage.res$greater you may track your problem from here. Weijun --- "Javerjung Sandhu" <jsandhu at="" bcgsc.ca=""> wrote: Dear list, I am getting the error listed below when i try to run the "gage" function within GAGE package: Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I have 1. Gene expression data consisting 4 libraries of "wildtype" and 4 of "knockout", totaling to 8 libraries. Each library contains expression values (normalized) for 6449 genes. 2. Phenotype file contains 2 phenotype classes: "wt" for wildtype and "ko" for knockout. 3. Gene set is custom made gene set. There are a total of 10 genesets containing 1406, 17, 10, 8, 150, 124, 91, 162, 58 and 290 genes respectively. I am able to read all the input files properly. I have done multiple GAGE analysis before but i didn't get error of this kind. Both the Gene set and Expression data are using the same gene ID system. Any help would be really appreciated. Thanks in advance. Thanks, Jung