Hi Group,
When I am runing GAIA I am getting an empty result file with just the
column names.
Previously I ran GAIA using the gist.RData and gist_markers.RData and I did
get the result for this.
The only difference between my file and gist file was that I dont have
chromosome 14 data in my file.Do you think that this is making the
difference?

The code that I am using is:

source("http://www.bioconductor.org/biocLite.R")
biocLite("gaia")
library(gaia)
marker_matrix<-read.table("markers2.txt",header = TRUE,sep = '\t')
marker_list<-load_markers(marker_matrix)

segmentation_matrix<-read.table("output_file_Tumor_wo_14_GAIA.txt",header=TRUE,sep='\t')
cnv_obj<-load_cnv(segmentation_matrix, marker_list,136)
GAIA<-runGAIA(cnv_obj,marker_list,output_file_name="Tumor_Gastric_GAIA.txt")

 glimpse of markers2 data:
probe chrom loc
1 1 604268
2 1 604287
3 1 689581
4 1 786483
5 1 792533
6 1 796956
7 1 807922

glimpse of output_file_tumor_wo_14_GAIA data:
Sample Chromosome Start.Position End.Position Num.Markers Label
GC20020876 1 604268 797005 6 0
GC20020876 1 807922 1145639 46 1
GC20020876 1 1149781 3558855 256 1
GC20020876 1 3563712 3563759 1 0
GC20020876 1 3568451 3981215 44 1
GC20020876 1 3988891 4769811 60 1

Waiting for your suggestions,
Thanks,
Viritha

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