Affymetrix is committed to providing its customers with the most accurate tools for analyzing GeneChip® Expression Analysis experiments. Since target sequences for GeneChip® expression arrays are derived from public databases, which are continuously updated, inconsistencies between probeset annotations and the actual sequences represented can arise. We have recently identified a small number of probesets (~26) on the Human Genome U95A Array whose target sequences no longer represent the intended transcripts accurately.

In order to remove these suspect probesets from your data sets, we have created a mask file that can be used during data analysis.

Applying this probe mask file towards analysis of HG-U95A arrays will remove all suspect probe sets from the analysis. All numerical analysis metrics (e.g. "Positive", "Negative", "Avg Diff", etc.) of affected probe sets will have values of zero, and the Absolute Call will be "Absent".

Download this mask file into the probe set information (i.e. Library) folder. To apply the probe mask file, select HG_U95A.msk under the Probe Mask tab of the Expression Call Settings window before running the analysis (for detailed information on applying probe masks, please refer to page 341 of the Microarray Suite 4.0 user guide).