Probe Profiler Software

Probe Profiler is a software solution for biologists who want to reduce variability of the data generated from the Affymetrix GeneChip system and to increase the overall quality and efficiency of the downstream analysis.

The Probe Profiler works in a data-driven fashion to:

1. Identify informative probe pairs,
2. Down weigh probe pairs that are subject to differential cross-hybridization effects (between Perfect match and Mismatch probes), or that don't detect signal,
3. Detect and correct for saturation artifacts, and outliers automatically.

Probe Profiler Benefits

• Improved reproducibility and sensitivity,
• Improved signal to noise of up to 6 times resulting in reliable detection of many low expressing genes,
• Substantial increase in productivity as it automatically detects and corrects for outliers and saturation effects, detects chip defects and low mRNA quality.
• Incorporation of statistical measures (confidence intervals, and p-values) in the result presentation providing a measure of quality and reliability of the data to the biologists.

Top

Probe Profiler Features

Diagnostics

Probe Profiler software provides diagnostic measures and plots to quickly assess the quality of chips and the mRNA preparation used in the hybridization.

The chip quality parameters include a) chip brightness and background noise, b) saturation and outlier plots, and c) cel outlier plot. mRNA diagnostics include indices on quality of hybridization spike-ins as well as the behavior of housekeeping genes among the cel files in any given experiment.

Saturation and Outlier Correction

Probe Profiler software automatically detect saturated and outlier probe pairs and corrects them. It also detects chip defects by looking at historical behavior of probe pairs and flagging any deviants.

Top

Probe Profiler Brochure in PDF format (415KB PDF).

The The

The software looks for consistency in behavior of the probe pairs as well as their efficiency in detecting message prior to assigning weights (Green line above)

Probe Probe Profiler presents overall trends in regard to saturation, cel outliers and chip brightness and background intensities for all the cel files in a given study.

I Quickly detect outliers, dust specs, smudges or chip scratches by viewing the false color images produced by Probe Profiler software.