CrossHybProbesets - kpeaton/altanalyze_wikitest GitHub Wiki

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.

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".