tag:blogger.com,1999:blog-10065122Tue, 22 Jul 2008 15:13:15 +0000http://www.stat.columbia.edu/~tzheng/tianblog/noreply@blogger.com (Tian Zheng)Blogger130125tag:blogger.com,1999:blog-10065122.post-7602879556321737104Tue, 22 Jul 2008 15:05:00 +00002008-07-22T11:13:15.369-04:00 New York Times published an article today on "Women Are Now Equal as Victims of Poor Economy". The whole article can be found here. I found the time plots used in this article is very interesting. It has some good graphing tactics: use of color/shade, for example and the Y axis is actually from 0-100%.http://www.stat.columbia.edu/~tzheng/tianblog/2008/07/up-and-downs-of-percentage-of-working.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-3765763407401526957Mon, 21 Jul 2008 21:15:00 +00002008-07-22T11:01:53.902-04:00"The Black Swan" is a best-seller by Nassim Nicholas Taleb, the author of another bigger best-seller "Fooled by Randomness." Both books received more than 300 reviews on Amazon.com. I flipped through the second book in the bookstore and thought it was an interesting book, especially for teaching statistics to curious and skeptical undergraduate students. Today, I stumbled over a special issue inhttp://www.stat.columbia.edu/~tzheng/tianblog/2008/07/black-swan.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-9107509378090906040Mon, 21 Jul 2008 20:38:00 +00002008-07-21T16:53:18.023-04:00This may be one of the most interesting articles from the president's column of AMSTAT news I have read recently. It is a reaction to an editorial of the Journal of American Medical Association that "impugning the integrity of medical science." As part of the proposed solution for the integrity problem in the pharmaceutical industry, it is suggested that clinical trial data collected by a http://www.stat.columbia.edu/~tzheng/tianblog/2008/07/solution-to-improve-integrity-in.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-362542123181325874Mon, 25 Feb 2008 17:38:00 +00002008-02-25T13:43:36.610-05:00In collaboration with Dr. Dimitris Anastassiou (EE, Columbia), we just published a paper on "Identification of gene interactions associated with disease from gene expression data using synergy networks" in BMC System Biology.http://www.stat.columbia.edu/~tzheng/tianblog/2008/02/identifying-gene-gene-interaction-that.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-5822432891179433211Tue, 19 Feb 2008 16:48:00 +00002008-02-19T11:56:28.642-05:00Here are some references on this technology for my own use. Global Identification of Human Transcribed Sequences with Genome Tiling Arrays Science 24 December 2004:Vol. 306. no. 5705, pp. 2242 - 2246 DOI: 10.1126/science.1103388 Paul Bertone,1* Viktor Stolc,1,2* Thomas E. Royce,3 Joel S. Rozowsky,3 Alexander E. Urban,1 Xiaowei Zhu,1 John L. Rinn,3 Waraporn Tongprasit,4 Manoj Samanta,2 Sherman http://www.stat.columbia.edu/~tzheng/tianblog/2008/02/tiling-arrays.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-5981943030232184926Tue, 19 Feb 2008 16:45:00 +00002008-02-19T11:47:56.161-05:00I always thought there was no function for standard deviation in R. Since in Splus, it was stdev() if I remember correctly. I never help.seached it. I only found out that there was one: sd().http://www.stat.columbia.edu/~tzheng/tianblog/2008/02/standard-deviation-function-in-r.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-6864805998793405854Tue, 13 Nov 2007 14:18:00 +00002007-11-13T09:23:00.757-05:00For a while, I have been using the setwd() command at the beginning of a project's code. This allows one to save data, graph, output easily to a project's result folder without typing long path names. Yesterday, I was using a contributed package in R that requires the access to R's temp directory. The exact location of this folder can be found out using the command tempdir(). It just happened http://www.stat.columbia.edu/~tzheng/tianblog/2007/11/temp-directory-and-working-director-of.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-6659259294767034504Mon, 12 Nov 2007 14:32:00 +00002007-11-12T09:36:26.506-05:00R graphical manuals (a nice collection of examples and codes) http://cged.genes.nig.ac.jp/RGM2/index.php?clear=all Codes from the book "R graphics" http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.htmlhttp://www.stat.columbia.edu/~tzheng/tianblog/2007/11/useful-websites-for-graphics-in-r.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-3219051988921509911Fri, 02 Nov 2007 23:24:00 +00002007-11-02T19:37:05.496-04:00Today, I need to permute many two-way tables of the same dimension (say 2 by 3) to carry out a test of independence. My data looks like a big matrix with each row corresponding to a two-way table (arranged by row). The permutation is just to draw a random 2 by 3 table given independence between the two dimensions, conditioning on the observed marginal distributions. I didn't find (or didn't have http://www.stat.columbia.edu/~tzheng/tianblog/2007/11/fast-permuting-r-by-c-two-way-tables.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-7639507545025002788Wed, 24 Oct 2007 13:12:00 +00002007-10-24T09:26:49.119-04:00Today, on CNN, it was said that some experts argued several epidemic consequences of global warming. One of them is tropical diseases are moving north. For example, malaria cases were reported in New Jersey. I found this claim is a little far-fetch. According to scientists, the temperature change due to global warming is about (1.33 ± 0.32 °F) during the last 100 years. The difference between http://www.stat.columbia.edu/~tzheng/tianblog/2007/10/tropical-infectious-diseases-moving.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-8257465693989531588Mon, 17 Sep 2007 23:11:00 +00002007-09-17T19:23:36.686-04:00Andrey Rzhetsky (a collaborator of mine) called me today. Among many things we discussed, he told me that our recent paper on estimating genetic overlap from phenotype data (time at diagnosis) had attracted quite a bit of popularity. It was the 24th most read paper of PNAS for the month of July 2007. And it was covered in MIT technology review and the Wired Science blog, among many other more http://www.stat.columbia.edu/~tzheng/tianblog/2007/09/probing-genetic-overlap-among-complex.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-3774069813060866074Sun, 16 Sep 2007 18:55:00 +00002007-09-16T15:00:58.076-04:00As Li pointed out, I had the wrong memory. I never aced any of these courses in my school days. BUT, I should have GOOGLED!!! :) That saying was published on May 11th, 1978. However, it was not proposed by Deng Xiaoping, despite the common perception. Deng only publicized it a lot. This is again a good example of Stigler's law of eponymy.http://www.stat.columbia.edu/~tzheng/tianblog/2007/09/correction-chair-mao-didnt-say.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-8211909843695548315Fri, 07 Sep 2007 22:32:00 +00002007-09-07T18:56:05.844-04:00I did not grow as a generation fully influenced by Mao Zedong. Actually, several days after I was born, he passed away. However, we still got to study quite a number of his quotes. One of them is "practice is the only way to validate the truth" (pardon my unpolished interpretation). 实践是检验真理的唯一标准。I have never given this quote much thought before yesterday. Yesterday, I received an email regardinghttp://www.stat.columbia.edu/~tzheng/tianblog/2007/09/chairman-mao-was-right.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-4072159393606944905Fri, 25 May 2007 20:51:00 +00002007-05-25T17:01:30.145-04:00Next time I go to visit some of my friends, I will pay more attention to their little black gaming devices, called PS3. It turns out the best computer processor of our times is used in it. It is the Cell Chip developed jointly by IBM, SONY and Toshiba. According to some very scientific study comparing the Cell Chip with conventionally designed chipset, the performance for chips with comparable http://www.stat.columbia.edu/~tzheng/tianblog/2007/05/i-want-playstation-3-for-research.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-9122344200891085304Tue, 22 May 2007 22:43:00 +00002007-05-22T18:44:39.694-04:00I came across this website that allows you to organize citations online. I think it is pretty neat. Especially it has Bibtex format right on the screen.http://www.stat.columbia.edu/~tzheng/tianblog/2007/05/citeulike.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-5744013625152240089Mon, 14 May 2007 15:58:00 +00002007-05-22T18:46:20.657-04:00Men are more likely to spend money on Mother's day than women (in both percentage and amount). This is a fact but this is also a nice example of "confounding" for intro stats. I heard about this in the news (people were joking about this as a "mom's boy" phenomenon) but can't find that exact news article today. I found the data on Mother's day 2005 (a pretty neat collection of numbers). Here is http://www.stat.columbia.edu/~tzheng/tianblog/2007/05/mothers-day-spending.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-5056810631624210383Wed, 09 May 2007 12:03:00 +00002007-05-09T08:16:34.186-04:00Anderson Copper 360 is a show on CNN that gives in-depth coverage of current events. In one of its recent airing, Anderson Copper discussed a question occurred during the recent Republican presidential debate: "do you believe in evolution?" One of the candidates added after the poll that he believed in evolution and also believed in God when watching things such as the sunset at Grand Canyon. http://www.stat.columbia.edu/~tzheng/tianblog/2007/05/divided-opinion.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-6154821343372357874Mon, 30 Apr 2007 23:12:00 +00002007-04-30T19:33:23.401-04:00PLoS Computational Biology's "Ten Simple Rules" series are pretty nice guidelines, including: Bourne PE (2005) Ten simple rules for getting published. PLoS Comp Biol 1: e57. Bourne PE, Chalupa LM (2006) Ten simple rules for getting grants. PLoS Comp Biol 2: e12. Bourne PE, Korngreen A (2006) Ten simple rules for reviewers. PLoS Comp Biol 2: e110. Bourne PE, Friedberg I (2006) Ten simple rules forhttp://www.stat.columbia.edu/~tzheng/tianblog/2007/04/ten-simple-rules-for-making-good-oral.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-594948865469564680Mon, 30 Apr 2007 03:29:00 +00002007-04-29T23:39:27.133-04:00I was frustrated with my little Lexmark printer for a while today. First, I can't print to it from my desktop (which I finally fixed it by re-installing the driver). Secondly, I totally forgot the PIN I set for its security. I tried everything I can think of for a 4-digit numeric PIN and realized how creative I must have been when setting it up and how lack of imagination I am now. I don't know http://www.stat.columbia.edu/~tzheng/tianblog/2007/04/10-most-common-passwords.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-1292365214660868890Sun, 29 Apr 2007 00:09:00 +00002007-04-28T20:26:55.031-04:00These are several ways of misusing data in science according to Charles Babbage, as mentioned in the following article. "Deception and dishonesty with data:fraud in science" by David Hand Significance, March 2007, pages 22-25 The part of this article I like most is the part where the author discussed that, despite the idealized image of scientists in the minds of the public, scientists are justhttp://www.stat.columbia.edu/~tzheng/tianblog/2007/04/hoaxing-forging-trimming-and-cooking.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-116443287850659945Sat, 25 Nov 2006 05:29:00 +00002007-04-30T11:24:01.023-04:00I always felt the spam emails I receive mimic the real emails in my inbox. I spoke to our web admin about this several months ago since I was worried that our mail server was infected by some viruses that "learn" the patterns of our real emails. Today, it just occured to me: it is NOT that the spams mimic our real emails. Rather, ONLY spams that look close to our real emails get pass our spam http://www.stat.columbia.edu/~tzheng/tianblog/2006/11/spams-that-mimic-real-emails.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-116399046934898711Mon, 20 Nov 2006 02:40:00 +00002006-11-19T21:41:09.350-05:00Here is a collection of style and bst files for journals. Some of them are pretty helpful.http://www.stat.columbia.edu/~tzheng/tianblog/2006/11/bst-files-for-journals.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-116388386369036237Sat, 18 Nov 2006 21:00:00 +00002006-11-19T21:39:26.896-05:00 Saw a nice venn diagram in Andrew's blog and loved it. But I sort feel the proportions do not agree with my perspective about the world and I love prettier colors. So I made one for myself.http://www.stat.columbia.edu/~tzheng/tianblog/2006/11/ser-venn-ity-prayer-redone.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-116381424964618163Sat, 18 Nov 2006 01:43:00 +00002006-11-17T20:44:09.656-05:00Found this online. I think it will be a nice tool for future simulaions.http://www.stat.columbia.edu/~tzheng/tianblog/2006/11/simped-for-pedigree-data-simulation.htmlnoreply@blogger.com (Tian Zheng)tag:blogger.com,1999:blog-10065122.post-116316932510836458Fri, 10 Nov 2006 14:34:00 +00002006-11-10T09:35:25.123-05:00I found this website accidentally. It is very interesting and contains a lot of information. http://www.math.yorku.ca/SCS/Gallery/milestone/http://www.stat.columbia.edu/~tzheng/tianblog/2006/11/milestones-in-history-of-data.htmlnoreply@blogger.com (Tian Zheng)