This page describes how to generate presence/absence calls of gene expression above background.
Instructions are available on the ProbeEffects portion of the download page.
| 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. |
| [log] logfile The name of the file to log progress, errors, etc. |
| [exon_annotation] probeset_annotation 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. |
| pgf_file The pgf file specifies the grouping of probes into probesets. See the annotation page to download. |
| clf_file The clf file describes the position of each probe on the chip. See the annotation page to download. |
| [exon_data] folder The folder storing the array cel files. |
| exon_cel_files A list of cel files, each array separated by a single "," and no spaces. |
| [output] presence_absence_output_file A prefix for the set of files created for presence/absence calls on each array. |
| [model] array_type The type of array analyzed. Here a value of "exon" should be specified. |
| method Background-correction method. One of (mat or median_gc) |
| calculate_presence_absence This value should be set to "true" to output presence/absence calls of gene expression. |
| mat_training_probe_type The probes used for training the background model. One of (background, full). Defaults to background. |