Metagene Projection Run on  Wed_Apr_18_15:11:26_2007
  
Model dataset: 
model.dataset.table
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/ALL_only.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/ALL_only.cls
column.subset ALL
column.sel.type samples
thres 20
ceil 1e+05
fold 8
delta 800
norm 6
  
Test dataset: 1
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.maxed.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.cls
column.subset c(1, 2, 13, 18, 27, 29, 39, 44, 45, 47, 49)
column.sel.type samples
thres NULL
ceil NULL
norm 6
   
Test dataset: 2
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.cls
column.subset c(2, 3, 4, 5, 6, 7, 8, 9, 10)
column.sel.type samples
thres 20
ceil 1e+05
norm 6
   
Test dataset: 3
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Armstrong_et_al.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Armstrong_et_al.cls
column.subset c(25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44)
column.sel.type samples
thres 20
ceil 1e+05
norm 6
   
Test dataset: 4
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.maxed.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.cls
column.subset c(5, 10, 14, 19, 22, 28, 37, 38, 43, 48, 52)
column.sel.type samples
thres NULL
ceil NULL
norm 6
   
Test dataset: 5
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Chiaretti_et_al.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Chiaretti_et_al.cls
column.subset ALL
column.sel.type samples
thres 20
ceil 1e+05
norm 6
   
Test dataset: 6
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.cls
column.subset c(12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31)
column.sel.type samples
thres 20
ceil 1e+05
norm 6
   
Test dataset: 7
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Yeoh_et_al.cls
column.subset c(42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61)
column.sel.type samples
thres 20
ceil 1e+05
norm 6
   
Test dataset: 8
V1
gct.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.maxed.gct
cls.file c:/CGP2006/MPM/Software_and_Examples/Leukemia2/Fine_et_al.cls
column.subset c(6, 9, 15, 16, 17, 20, 23, 24, 25, 30, 33, 42, 51)
column.sel.type samples
thres NULL
ceil NULL
norm 6
   
Parameters:
identifier= Leukemia2.ALL
k.proj= 5
alg= NMF.div
niter= 2000
seed= 1234
nchar.phen= 9
postprojnorm= TRUE
heatmap.row.norm= FALSE
heatmap.cmap.type= 6
high.conf.thres= 0.3
output.dir= c:/CGP2006/MPM/Software_and_Examples/Leukemia2/
col= green2 yellow2 paleturquoise2 chocolate3 blue2 green2 yellow2 paleturquoise2 paleturquoise4 chocolate3 chocolate4 blue2 blue4
symbs= 22 22 22 22 22 21 23 24 21 25 21 23 21
symbol.scaling= 0.55
kernel= radial
cost= 1
gamma= 0.05
theta= 0
lambda= 1
model.set.refinement= TRUE
