[BioC] A error in GAGE analysis

[Luo Weijun]

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