https://sourceforge.net/p/altanalyze/wiki/CrossHybProbesets/Recent changes to CrossHybProbesetsenSat, 01 Feb 2014 01:07:07 -0000https://sourceforge.net/p/altanalyze/wiki/CrossHybProbesets/<div class="markdown_content"><h3 id="how-can-i-remove-probesets-with-sequence-that-aligns-to-multiple-genomic-loci-from-my-analysis"><em>How can I remove probesets with sequence that aligns to multiple genomic loci from my analysis?</em></h3> <p><em><strong>Answer</strong></em>: Whether you are using the graphical user interface or <a class="" href="/p/altanalyze/wiki/CommandLineMode/">command-line mode</a>, you can choose to remove genomic cross-hybridizing probesets. </p> <p>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: </p> <p><img alt="" src="http://www.genmapp.org/AltAnalyze/image/SelectCELfiles.jpg" rel="nofollow" /></p> <p>You can also do this in the <a class="" href="/p/altanalyze/wiki/CommandLineMode/">command-line</a> by adding the flag "--noxhyb yes" which instructs <a class="" href="/p/altanalyze/wiki/AltAnalyze/">AltAnalyze</a> to exclude cross-hybridizing probesets. These annotations are obtained from annotation files produced for the <a class="" href="http://biogibbs.stanford.edu/~yxing/MADS/Annotation.html" rel="nofollow">MADS software</a>. </p> <p>You can also do this yourself by downloading the Affymetrix probeset annotation file for your exon array (e.g., <a class="" href="http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st" rel="nofollow">HuEx-1_0-st-v1.na31.mm9.probeset.csv</a>) from the <a class="" href="http://www.affymetrix.com/support/technical/byproduct.affx?" rel="nofollow">Affymetrix website</a> and identifying probesets with several probes that cross-hybridize according to the column "number_cross_hyb_probes". </p></div>AnonymousSat, 01 Feb 2014 01:07:07 -0000https://sourceforge.netcb2c28d1d98ea08265fdee442d0c92328122b4f0