Hi Steve, Thanks for the rapid response. We may be able to fit in a small sub- analysis into a student thesis project - and will definitely get back to you if we pursue that. Certainly, the outlier probesets in arrays with artifacts will have quite large or near-zero intensity levels - which when transformed into z-scores will bias the z's of all the other probesets due to their influence on the mean over all probesets. Once we identify those probesets, we can go into the SCAN expression set to see what happened to them. For now, we'll stick with removal of bad arrays based on NUSE results. Best, Leif Sent from my iPhone On Sep 25, 2013, at 7:17 AM, "Steve Piccolo" <stephen.piccolo at="" hsc.utah.edu=""> wrote: > Hi Leif, > > Thanks for your email. We have not yet done a formal evaluation to address > how well SCAN.UPC can address artifacts and degraded hybridization, etc. > So for the time being we would recommend that you use NUSE and/or other > quality-control tests before applying SCAN.UPC. However, when summarizing > at the gene/probeset level, we use a 10% trimmed mean, so this may be > adequate in many cases for excluding outlier probes due to streaks, > blotches, etc. > > We have considered to use the signal-to-noise ratio or some other metric > that can be derived from the SCAN.UPC calculations as a way to measure > sample quality. But so far we haven't implemented that. > > If by chance you decide to do a formal evaluation along these lines, we'd > be happy to discuss it with you. > > Thanks, > -Steve > > > > On 9/25/13 4:00 AM, "bioconductor-request at r-project.org" > <bioconductor-request at="" r-project.org=""> wrote: > >> Message: 20 >> Date: Tue, 24 Sep 2013 07:55:34 -0500 >> From: "Leif Peterson" <leifepeterson at="" sbcglobal.net=""> >> To: <bioconductor at="" r-project.org=""> >> Subject: [BioC] SCAN.UPC vs NUSE >> Message-ID: <001801ceb925$5cdd0440$16970cc0$@sbcglobal.net> >> Content-Type: text/plain >> >> Prior to using SCAN.UPC and ComBat, we originally ran NUSE (in AffyPLM) >> and >> removed Affy Hu-133A arrays for which the NUSE criterion was > 1.05. We >> are wondering whether use of SCAN.UPC without pre-filtering by NUSE would >> be >> sufficient? Also, regarding artifacts and degraded hybridization regions >> on >> chips (visible in AffyPLM Residual plots in the form of streaks, blotches, >> hot spots, etc.), we are wondering what SCAN.UPC would do with such >> perturbations? >> >> >> Leif Peterson >> >> HMRI, Houston > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://urldefense.proofpoint.com/v1/url?u=https://stat.ethz.ch/mail man/listinfo/bioconductor&k=UOImn7AELLifIPWdtrbUhQ%3D%3D%0A&r=Ze6Sr1k6 6Qh70lnaKeD8j7SX4gJQBNcp9tY8NB24x6o%3D%0A&m=cVf4N6AXuadcZqY%2BUZVK3krt oItRKZh4eYk0ftSpjyY%3D%0A&s=46b5d121054b5019014cace3661614d9f052048d3b 776e73c661cfbdbe6d73b6 > Search the archives: https://urldefense.proofpoint.com/v1/url?u=http ://news.gmane.org/gmane.science.biology.informatics.conductor&k=UOImn7 AELLifIPWdtrbUhQ%3D%3D%0A&r=Ze6Sr1k66Qh70lnaKeD8j7SX4gJQBNcp9tY8NB24x6 o%3D%0A&m=cVf4N6AXuadcZqY%2BUZVK3krtoItRKZh4eYk0ftSpjyY%3D%0A&s=3fa573 1783cd99765d6bb08e872bea12907e8084b9e683a2445553b09e6e89ab Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work For?" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.