different rf-ace behaviors between versions

Hi Timo,

I tried running the biovis feature on the new rf-ace release and got 
"No features match the specified target identifier '0'"
while an older release, r169, ran okay. 
I will try it with an older TCGA dataset too.

Thanks,
Jake

What steps will reproduce the problem?
1. feature matrix 
/proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv 7577x500 
run rf-ace_r227 (latest as of 07/12)

/proj/ilyalab/TCGA/rf-ace_r227/bin/rf_ace -I 
/proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv -i 0 -n 
500 -m 1000 -p 20 -t 1 -O associations_0.out

 --------------------------------------------------------------- 
| RF-ACE -- efficient feature selection with heterogeneous data |
|                                                               |
|  Version:      RF-ACE v0.5.8, July 8th, 2011                  |
|  Project page: http://code.google.com/p/rf-ace                |
|  Contact:      timo.p.erkkila@tut.fi                          |
|                kari.torkkola@gmail.com                        |
|                                                               |
|              DEVELOPMENT VERSION, BUGS EXIST!                 |
 --------------------------------------------------------------- 

Reading file 
'/proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv'
File type is unknown -- defaulting to Annotated Feature Matrix (AFM)
AFM orientation: features as rows
No features match the specified target identifier '0'

run older rf-ace version:
 rf-ace_r1169 (symlink)
/proj/ilyalab/TCGA/rf-ace/bin/rf_ace -I 
/proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv -i 0 -n 
500 -m 1000 -p 20 -t 1 -O associations_0.out

 --------------------------------------------------------------- 
| RF-ACE -- efficient feature selection with heterogeneous data |
|                                                               |
|  Version:      RF-ACE v0.3.1, June 24th, 2011                 |
|  Project page: http://code.google.com/p/rf-ace                |
|  Contact:      timo.p.erkkila@tut.fi                          |
|                                                               |
|              DEVELOPMENT VERSION, BUGS EXIST!                 |
 --------------------------------------------------------------- 

Reading file 
'/proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv'
File type is unknown -- defaulting to Annotated Feature Matrix (AFM)
AFM orientation: features as rows

RF-ACE parameter configuration:
  --input      = /proj/ilyalab/Patrick/bioviscontest_dataset_2011_v2/data/rf.input.tsv
  --nsamples   = 500 / 500 (0% missing)
  --nfeatures  = 7576
  --targetidx  = 0, header 'C:GENO:chr16:67319257:chr16:67319257:67319257::'
  --ntrees     = 500
  --mtry       = 1000
  --nodesize   = 25
  --nperms     = 20
  --pthresold  = 1
  --output     = associations_0.out

Growing 20 Random Forests (RFs), please wait...
  RF 1: 500 nodes (avg. 1 nodes / tree)
  RF 2: 500 nodes (avg. 1 nodes / tree)
  RF 3: 500 nodes (avg. 1 nodes / tree)
  RF 4: 500 nodes (avg. 1 nodes / tree)
  RF 5: 500 nodes (avg. 1 nodes / tree)
  RF 6: 500 nodes (avg. 1 nodes / tree)
  RF 7: 500 nodes (avg. 1 nodes / tree)
  RF 8: 500 nodes (avg. 1 nodes / tree)
  RF 9: 500 nodes (avg. 1 nodes / tree)
  RF 10: 500 nodes (avg. 1 nodes / tree)
  RF 11: 500 nodes (avg. 1 nodes / tree)
  RF 12: 500 nodes (avg. 1 nodes / tree)
  RF 13: 500 nodes (avg. 1 nodes / tree)
  RF 14: 500 nodes (avg. 1 nodes / tree)
  RF 15: 500 nodes (avg. 1 nodes / tree)
  RF 16: 500 nodes (avg. 1 nodes / tree)
  RF 17: 500 nodes (avg. 1 nodes / tree)
  RF 18: 500 nodes (avg. 1 nodes / tree)
  RF 19: 500 nodes (avg. 1 nodes / tree)
  RF 20: 500 nodes (avg. 1 nodes / tree)
20 RFs, 10000 trees, and 10000 nodes generated in 94.17 seconds (106.191 nodes 
per second)

Association file created. Format:
TARGET   PREDICTOR   P-VALUE   IMPORTANCE   CORRELATION

Done.

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?

Please provide any additional information below.
Original issue reported on code.google.com by jlin...@gmail.com on 12 Jul 2011 at 4:37
gsethi / rf-ace

different rf-ace behaviors between versions #7
