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",hea der=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 [[alternative HTML version deleted]]