The scores file lists the Q values [presented as -log10(q)], G scores,

average amplitudes among aberrant samples, and frequency of aberration,

across the genome for both amplifications and deletions. The scores file is

viewable with the Genepattern SNPViewer module and may be imported into the

The segmented copy number is a pdf file containing a colormap image of the

segmented copy number profiles in the input data.

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The amplification pdf is a plot of the G scores (top) and Q values (bottom)

with respect to amplifications for all markers over the entire region

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with

respect to deletions for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

Tables of basic information about the genomic regions (peaks) that GISTIC

determined to be significantly amplified or deleted. These describe three

kinds of peak boundaries, and list the genes contained in two of them. The

region start and region end columns (along with the chromosome column)

delimit the entire area containing the peak that is above the significance

level. The region may be the same for multiple peaks. The peak start and end

delimit the maximum value of the peak. The extended peak is the peak

determined by robust, and is contained within the wide peak reported in

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

A table of per-arm statistical results for the data set. Each arm is a row

in the table. The first column specifies the arm and the second column

counts the number of genes known to be on the arm. For both amplification

and deletion, the table has columns for the frequency of amplification or

deletion of the arm, and a Z score and Q value.

A table of chromosome arm amplification levels for each sample. Each row is

a chromosome arm, and each column a sample. The data are in units of absolute