How can I remove probesets with sequence that aligns to multiple genomic loci from my analysis?
Answer: Whether you are using the graphical user interface or command-line mode, you can choose to remove genomic cross-hybridizing probesets.
If you are working in the graphical user interface, you can eliminate these by selecting "Remove probesets with a large cross-hybridization score" option when selecting CEL files to analyze:
You can also do this in the command-line by adding the flag
--noxhyb yes which instructs AltAnalyze to exclude cross-hybridizing probesets. These annotations are obtained from annotation files produced for the MADS software[Xing2008].
You can also do this yourself by downloading the Affymetrix probeset annotation file for your exon array (e.g., HuEx-1_0-st-v1.na31.mm9.probeset.csv) from the Affymetrix website and identifying probesets with several probes that cross-hybridize according to the column "number_cross_hyb_probes".