King Oedipus Essays 1 - 30 Anti Essays

Thursday, October 12, 2017 12:53:44 AM






Error Statistics Philosophy " data-medium-file="https://errorstatistics.files.wordpress.com/2014/05/toilet-fireworks-by-stephenthruvegas-on-flickr.jpg?w=300" data-large-file="https://errorstatistics.files.wordpress.com/2014/05/toilet-fireworks-by-stephenthruvegas-on-flickr.jpg?w=362" class="size-thumbnail wp-image-14882" src="https://errorstatistics.files.wordpress.com/2014/05/toilet-fireworks-by-stephenthruvegas-on-flickr.jpg?w=150&h=133" alt="Potti training" width="150" height="133" srcset="https://errorstatistics.files.wordpress.com/2014/05/toilet-fireworks-by-stephenthruvegas-on-flickr.jpg?w=150&h=133 150w, https://errorstatistics.files.wordpress.com/2014/05/toilet-fireworks-by-stephenthruvegas-on-flickr.jpg?w=300&h=266 300w" sizes="(max-width: 150px) 100vw, 150px" /> Having piled all the blame on Anil Potti, Potti is now free to deny any blame as well. Scarcely a disincentive to avoid “disregarding accepted scientific methodology” in the future. I will comment later on. Share your thoughts. The Federal Register Notice is here. For background and key links to this case, please see on this blog: Baggerly & Coombes. (2009). Deriving Chemosensitivity from cell lines: Forensic Bioinformatics and reproducible research in high-throughput Biology, Ann. of Appl. Stat.Vol. 3, No. 4 (Dec. 2009), pp. 1309-1334. [Starter Kit Webpage supplement for B&C 2009:http://bioinformatics.mdanderson.org/Supplements/ReproRsch-All/Modified/StarterSet/index.html] Baggerly, Coombes, Neeley (2008) Run Batch Effects Potentially Compromise the Usefulness of Genomic Signatures for Ovarian Cancer. JCO March 1, 2008:1186-1187. Coombes, Wang & Baggerly. (2007). “Microrrays: retracing steps.” Nat. Med. Nov 13(11):1276-7. Dressman, Potti, Nevins & Lancaster (2008) In Reply. JCO March 1, 2008:1187-1188 McShane (2010). NCI Address to lnstitute of Medicine Committee Convened to Review Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials. PAF 20. Micheel et al (Eds) Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Institute of Medicine (2012). Evolution of Translational Omics: Lessons Learned and the Path Forward. Nat. Acad. Press. Potti et al.(2006). Genomic signatures to guide the use of chemotherapeutics. Nat. Med. Nov 12(11):1294-300. Epub 2006 Oct 22. Potti and Nevins (2007) Reply to Coombes, Wang & Baggerly Nat. Med. Nov 13(11):1277-8. I welcome constructive comments for 14-21 days. If you wish to have a comment of yours removed during that time, send me an e-mail. Cancel reply. A sad situation. Particularly odd is the antiseptic verbiage of the “official report”, no doubt the work product of highly paid lawyers and minimum wage wordsmiths. This person, who was obviously caught red-handed, should never again darken the door of any research establishment in the world, period. I have a feeling that “the word is on the street now” regarding this whole sorry debacle so future employment in academia or industry is perhaps now very unlikely with P. James: It is troubling. Your P. After reading through, it is still not clear to me whether the original analysis was reproducible from the papers. If it wasn’t, the fraud isn’t really relevant since there was no reason to take the papers seriously to begin with. He should have been refused future funding and ignored for that reason (along with everyone else who has a consistent history of producing useless research reports). If even the analysis was non-reproducible from the description, this should have easily order essay online cheap liberal versus marxist feminism and women in corporate america up during routine independent replication attempts. These are required before testing something on patients, right? That it required a whisteblower would indicate deeper problems with the medical research community. As I said, it is not clear to me whether the original analysis was described well enough in the papers. Anoneuoid: “If even the analysis was non-reproducible from the description, this should have easily come up during routine independent replication attempts. These are required before testing something on patients, right?” You live in a charmed world, or what most people consider a world with normal expectations for clinical trials. When Baggerly and Coombes could not replicate the results and discovered flagrant data errors, they wrote a letter to Nature to which Potti responded: “If they’d only followed the way I got my results they would have obtained them as well!” His way was basically to throw out anything that didn’t look good and double up on on the data points that worked (I am not kidding, read Baggerly and Coombes, and whistleblower Perez). Medical journals wouldn’t publish Baggerly and Coombes’ paper, deeming it altogether too negative! (Who wants to read negative stuff? ) Finally Efron published it in the Annals of Applied Stat. Meanwhile, the trials based on the fraudulent prediction model were proceeding apace. Only after something like 30 statisticians signed a letter in protest were the trials halted. But only temporarily. The internal investigation at Duke (whose members were not given the Baggerly and Coombes critique, nor told of the whistleblower) decided everything was hunky dory, and the patients were called back to resume their “personalized” cancer therapy. Even aside from the deeper problems with the “validation” of the prediction model, the researchers often entered data in backwards so that patients got the treatment deemed least effective (on patients with tumors like theirs). Patients weren’t told of any of the alleged problems. Had Potti not lied on his CV about getting a Rhodes scholarship,the fraud wouldn’t even have been investigated, at least not when it finally was. The episode is ghastly. Retraction Watch quotes a Buy essay online cheap snowboarding trip official relieved at these findings. A VP for marketing and communications for “Duke Medicine”: “We are pleased with the finding of research misconduct by the federal Office of Research Integrity related to work done by Dr. Anil Potti. We trust this will serve to fully absolve the clinicians and researchers who were unwittingly associated with his actions, and bring closure to others who were affected”. I don’t get it. Links from your post on whistleblower Perez (the letter published in The Cancer Letter) show that many researchers and administrators at Duke knew about cheap write my essay the effects gatorade has on the body complaints by Potti’s student: “The three-page document was penned by Bradford Perez, then a third-year medical student … Instead of rewarding the student’s brilliance with a plaque and a potted plant, Potti’s collaborator and protector, Joseph Nevins—aided by a phalanx of Duke deans—pressured the young man to refrain from making a final complaint and reporting the matter to HHMI”. http://www.cancerletter.com/articles/20150109_1. The new finding implicates and doesn’t “absolve” them. Exactly right, e. berk: As stated at Retraction Watch: ” Update, 1:45 p.m. Eastern, 11/8/15: In a statement, Doug Stokke, vice president of marketing order essay online cheap liberal versus marxist feminism and women in corporate america communications for Duke Medicine, tells us: We are pleased with the finding of research misconduct by the federal Office of Research Integrity related to work done by Dr. Anil Potti. We trust this will serve to fully absolve the clinicians and researchers who were unwittingly associated with his actions, and bring closure to others who were affected. ” The ORI report in itself does nothing to absolve anyone else, as you correctly note. The ORI investigation focused on Potti’s work, a single researcher alone, as their investigations typically do. The ORI report mentions nothing about other researchers. This is nothing but more shameful marketing from Duke personnel, obfuscating the situation with hand waving and double speak as was done for years as Baggerly and Coombes tried to shed light on this situation. The clinical trials patients’ court cases have been adeptly settled out of court order essay online cheap liberal versus marxist feminism and women in corporate america non-disclosure agreements, and now with this narrowly focused ORI investigation report, Duke marketing personnel present the spin that this somehow absolves others who were not under scrutiny by the ORI. Do not trust the proclamations of such a spin-meister. Closure was brought about in the case of Joseph Nevins by orchestrating a quiet retirement exit. Any groups at Duke still using the methodology involved in the Potti-Nevins et al. fiasco still require careful scrutiny. If the methodology was so good, why did Potti have to fiddle with so many bits of data (as outlined in the ORI report)? Steven: Totally agree. Anyone who wants to hear about how “unwitting” his associates were should read the whistleblower letter by Perez. He was writing directly to Nevins and shared his worries with various deans. But I’ not sure why the NCI, when already suspicious of Pott, gave him so many, many chances to fiddle with the data, and try and try again to show their model “worked”? Readers unfamiliar with the case might look at the Lisa McShane (from the NCI) statement: http://iom.nationalacademies.org/ The NCI gave the Duke group so many chances because the NCI biostatistics group involved were a talented, fair and honest bunch of researchers. When the Duke group wanted to start clinical trials, they already had publications in some fine glossy journals. The Duke group presented their methods and findings to the NCI with an apparently stellar set of references and used language that made it all seem so good. The NCI had King Oedipus Essays 1 - 30 Anti Essays check into the methods, since human trials were proposed. The Duke group provided reams of documentation so reading all of it, making notes, comparing across documents etc. would have taken many days of effort. The Duke group provided some, but not all computer programs used King Oedipus Essays 1 - 30 Anti Essays produce the results in the papers they cited in their clinical trials grant proposals. The NCI group had to figure out how to use the suite of under-documented code. Some of the code was provided in a binary format, without source code, so the NCI had to just play around with that code, to try and figure out analysis paper freedom writers was buy essay online cheap study on work related stress on inside that “black box” (TreeProfiler). The NCI group had to rewrite some of their own code to do some analyses that the Duke group could not provide computer code for (e.g. Bayesian classification tree – see PAF Document 11.pdf). As the NCI group started noticing problems, and contacting Duke about them, there was much to-and-fro letter writing, emailing and the like. Thus it took many months for the NCI to amass enough findings to clearly demonstrate the problems involved. Because the NCI group gave the Duke group so many, many chances, the NCI group eventually ended up with plenty of evidence to clearly present their case for shutting down the trials, as they did at the IOM hearings. Short of that, the marketing skills of Duke personnel would have cast a dark light on the NCI as just another heavy handed government agency interfering with such a fine group just trying to save people’s lives with such great new methodology. Duke did at least two things wrong. 1. They messed up the data set building (Potti messed up a sort/merge so data was not aligned properly.) It was technical mistake by a person not trained in data processing. There was also a management mistake. No one was checking the work of Potti. 2. In the face of real evidence Duke was wrong with their data processing, still no one checked the work of Potti, then they stonewalled and worse. My understanding is that the research team was effectively disbanded at the time the problems were figured out. There was a systems problem. The real problem is that research at writing an essay and this writing service provided is more or less a cottage industry. A small team does everything with many single points of possible failure and essentially NO OVERSIGHT. It is like auto manufacture before the assembly line. In contrast, drug discovery within a drug company is a large-scale, highly integrated process with high quality research and effective oversight. The Institute of Medicine more or less said that typical university research labs are not organized to do sound, reproducible research. Normally university findings get tested and filtered by drug companies. See Begley and Ellis Nature 2011 for a veritable catalogue of poor statistical practice. Research in universities is most typically “cottage industry”. That fine for training, but it does not produce reliable results. A major fault was the university system. Yes, Potti failed, but he failed because of poor system design. He was not trained to do the work he was doing and buy essay online cheap thl case study 8 was no oversight. To my knowledge, the university research system has not been fixed at all. Duke was quick to throw Potti under the bus once it was discovered he fudged is resume. They did not admit they had a systems problem.

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