Question: A error in GAGE analysis
0
gravatar for Javerjung Sandhu
7.5 years ago by
Javerjung Sandhu200 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 [[alternative HTML version deleted]]
gage • 660 views
ADD COMMENTlink modified 7.5 years ago by Luo Weijun1.5k • written 7.5 years ago by Javerjung Sandhu200
Answer: A error in GAGE analysis
0
gravatar for Luo Weijun
7.5 years ago by
Luo Weijun1.5k
United States
Luo Weijun1.5k wrote:
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
ADD COMMENTlink written 7.5 years ago by Luo Weijun1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 134 users visited in the last hour