25.4.1 Log2Ratio Covariates Dataset

The first of two spreadsheets that are created by importing segmenting results is a covariates data set. This spreadsheet contains the average log2 ratio value for each sample within each segment of markers. In this spreadsheet, the rows correspond to the samples, the columns correspond to the overall segments which have been determined, and the data are the average log2 ratio values.

Each column is identified by the chromosome number, the beginning marker, and the ending marker. The markers are identified by chromosome position.

25.4.2 Log2Ratio Segments Dataset

The second of two spreadsheets that are created by importing segmenting results is a segments data set. This spreadsheet contains columns for the chromosome name, segment start position, segment end position, segment mean, and the segment length in number of markers. Spreadsheet rows correspond to samples.

If the LogR ratios used in the analysis were exported from a BeadStudio project, the data from this spreadsheet can be exported and viewed in BeadStudio. To export the spreadsheet, select from the spreadsheet menu File->Save As Comma-Delimited Text File. For details about how to import this data into BeadStudio, see 25.8.1 and D.3.4.

25.4.3 Wiggle Track (WIG) File

You may optionally choose to output a Wiggle Track (WIG) format file for Genome Browser import. This file identifies the segments which were found from the segmenting algorithm. For details about how to import a WIG file in a genome viewer, see 25.8.2 or 25.8.3.