Output presence/absence calls


This page describes how to generate presence/absence calls of gene expression above background.

Step 1: Download the ProbeEffects program

Instructions are available on the ProbeEffects portion of the download page.

Step 2: Create a parameter file

A parameter file specifies the following types of information
A log file to store the progress of the computation and to output any error messages.
Exon array annotation, including pgf, clf and probeset annotation files. These can be downloaded from the annotation page.
The exon array data.
An output file stores the resulting presence/absence calls in each sample.
The model parameters specify a choice of background correction method.


We provide several sample parameter files which can be modified. Detailed descriptions of the para meters are given below.

***Note that flags and parameter values are separated by tabs***

MAT presence/absence calls.
Median GC presence/absence calls.

The name of the file to log progress, errors, etc.
The probeset annotation file specifies the grouping of probesets into transcript clusters and the level of annotation supporting each probeset. See the annotation page to download.
The pgf file specifies the grouping of probes into probesets. See the annotation page to download.
The clf file describes the position of each probe on the chip. See the annotation page to download.
The folder storing the array cel files.
A list of cel files, each array separated by a single "," and no spaces.
A prefix for the set of files created for presence/absence calls on each array.
The type of array analyzed. Here a value of "exon" should be specified.
Background-correction method. One of (mat or median_gc)
This value should be set to "true" to output presence/absence calls of gene expression.
The probes used for training the background model. One of (background, full). Defaults to background.