Dear all,  I have identified two lists of differential expressed gene from the same expression data but treated with different normalisation methods. List A contains 995 genes and list B contains 2400 genes. More than nine hundreds genes are overlapped between two lists, namely most of genes in list A are also included in list B. The idea is to check whether list B is better than list A.  In addition to visualisation approach (like hierarchical clustering heatmap) or biological interpretations,  I am wondering is there any other statistical approach available to compare two differential expressed gene lists?  I would appreciate any advice, or pointers to any references for this!  Bests, Qinghua  ----- 转发邮件 ---- 发件人： qinghua xu <xy0702cy@yahoo.com.cn> 收件人： Francois Pepin <fpepin@cs.mcgill.ca>; bioconductor@stat.math.ethz.ch 抄 送： qinghua.xu@as.biomerieux.com 发送日期： 2009/12/18 (周五) 10:55:11 上午 主 题： 回复： 回复： [BioC] : Patent issues of classification algorithms Dear  Francois,  Thank you so much for this very helpful information. It is good to know that there is no patent concern for the basic classification methods. At this moment, our goal is just to pulish some results of microarray study, rather than commercializing a test. Not yet.  As working in an IVD company, I was reminded to be careful with intellectual property protection issue.  Thanks again!  Bests Qinghua ________________________________ 发件人： Francois Pepin <fpepin@cs.mcgill.ca> 抄 送： bioconductor@stat.math.ethz.ch; Sean Davis <seandavi@gmail.com>; qinghua.xu@as.biomerieux.com 发送日期： 2009/12/16 (周三) 3:00:41 上午 主 题： Re: [BioC] : Patent issues of classification algorithms Dear Qinghua, I don't think you should concern yourself too much with patents on most classification methods. Yes, there might be lots of SVM patents in a biomedical field, but the basic method for SVM is not patented and the same is true for almost all other methods. Unless something malicious was going on, the license field should tell you if there is anything you should worry about. For example, the siggenes packages says that a paid license is needed for non-academic users. But as I said, I don't think any of the basic classification methods in R (including in e0171) are patented and I would not worry about it in a publication. If you were planning on commercializing a test, it could be worth checking more heavily about it.  I would expect those patents are of the sort, using genes X,Y,Z with this algorithm with these parameters to solve this problem. Just using the same algorithm would probably not be covered by those patents. Still, if there is money at stake, you would be better off contacting someone specialized in the field. Francois On 12/14/2009 10:49 PM, qinghua xu wrote: > Dear Sean, > [[elided Yahoo spam]] > > I think the main concern is not the citation issue. That should be OK. I have rapidly checked the "GNU GENERAL PUBLIC LICENSE" under which R packages are released. If I understand correctly, it is more about COPYING, DISTRIBUTION and MODIFICATION program itself, rather than the outputs from using program. > > Take the famous package (e0171) as an example. Without doubt, it is under the licence GPL-2, however, I also find massive patents of SVM application in the biomedical field.  Maybe, it is rather a question for intellectual property protection specialists. > > Thanks again! > > Qinghua > > > > ________________________________ > å‘件人： Sean Davis<seandavi@gmail.com> > > 抄 é€ï¼š bioconductor@stat.math.ethz.ch; qinghua.xu@as.biomerieux.com > å‘é€æ—¥æœŸï¼š 2009/12/14 (周一) 8:38:58 下åˆ > 主 题： Re: [BioC] Patent issues of classification algorithms > > >> Dear all, >> >> I would like to know is there any patent related concern when try to publish a microarray study using different classification algorithms, like KNNs, Random Forest, Support Vector Machine and so on? >> > [[elided Yahoo spam]] > > A couple of places to look: > > In the DESCRIPTION of each package available for R, there is a license > line that may be useful for determining the license under which the > software is released.  More importantly, though, is probably the > citation() entry, which gives the citations for the package that > should be cited if the package is used in a publication. > > As for patents, I'm not sure how important that is from a user > perspective; perhaps others want to comment here. > > Sean > > ________________________________ > 好玩贺å¡ç­‰ä½ å‘，邮箱贺å¡å…¨æ–°ä¸Šçº¿ï¼ > > >       ___________________________________________________________ >    好玩贺å¡ç­‰ä½ å‘，邮箱贺å¡å…¨æ–°ä¸Šçº¿ï¼ > >     [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ________________________________ å¥½çŽ©è´ºå¡ç­‰ä½ å‘ï¼Œé‚®ç®±è´ºå¡å ¨æ–°ä¸Šçº¿ï¼ ___________________________________________________________ å¥½çŽ©è´ºå¡ç­‰ä½ å‘ï¼Œé‚®ç®±è´ºå¡å ¨æ–°ä¸Šçº¿ï¼ [[alternative HTML version deleted]]