Broad Values By Arm (broad_values_by_arm.txt)

A gene-level table of copy number values for all samples. Each row is the

data for a gene. The first three columns name the gene, its NIH locus ID,

and its cytoband - the remaining columns are the samples. The copy number

values in the table are in units of (copy number -2), so that no

amplification or deletion is 0, genes with amplifications have positive

values, and genes with deletions are negative values. The data are converted

from marker level to gene level using the extreme method: a gene is assigned

the greatest amplification or the least deletion value among the markers it

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number data similar to the

output, but using only broad events with lengths greater than the  broad

length cutoff. The structure of the file and the methods and units used for

the data analysis are otherwise identical to

Broad Data By Genes (broad_data_by_genes.txt)

output, but using only focal events with lengths greater than the  focal

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for

all samples. There is a row for each gene. The first three columns name the

gene, its NIH locus ID, and its cytoband - the remaining columns are the

samples. A table value of 0 means no amplification or deletion above the

threshold. Amplifications are positive numbers: 1 means amplification above

the amplification threshold; 2 means amplifications larger to the arm level

amplifications observed for the sample. Deletions are represented by

negative table values: -1 represents deletion beyond the threshold; -2 means

deletions greater than the minimum arm-level deletion observed for the sample.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number

-2) used to distinguish the high level amplifications (+/-2) from ordinary

contains three columns: the sample identifier followed by the low (deletion)