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)

and high (amplification) cutoff values. The cutoffs are calculated as the

minimum arm-level amplification level less the deletion threshold for

deletions and the maximum arm-level amplification plus the amplification

A list of copy number segments describing just the focal events present in

the data. The segment amplification/deletion levels are in units of (copy

number -2), with amplifications positive and deletions negative numbers.

Focal Input To Gistic (focal_input.seg.txt)

An image showing the correlation between gene counts and frequency of copy

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

A file indicating the position of the confidence intervals around GISTIC

peaks that can be loaded as a track in a compatible viewer browser such as

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)