Dear Ting-Yuan Thank you so much for your help. I still have one more question for you. I am trying to construct venn diagram in r-programming but could not success. For example: i have 100 genes in set A only, 50 genes in set B only and there are 25 common genes in both set (in intersection). So, would you mind to suggest how it is possible to construct venn diagram in r-programming. Thank you. With best regards. Amrit Karki [[alternative HTML version deleted]]

Hi Amrit, On Jul 15, 2009, at 12:26 AM, amrit karki wrote: > Dear Ting-Yuan > Thank you so much for your help. I still have one > more question for you. I am trying to construct venn diagram in > r-programming but could not success. For example: i have 100 genes in > set A only, 50 genes in set B only and there are 25 common genes in > both set (in intersection). So, would you mind to suggest how it is > possible to construct venn diagram in r-programming. One thing you can try to do is look through the bioconductor archives to see if your question has already been answered (instead of, say, reposting your question multiple times). Gmane can help you do this with ease. In fact, this thread just popped up: http://thread.gmane.org/gmane.science.biology.informatics.conductor/23 918 -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

It is not so easy to use vennCounts unless you have an incidence matrix with the union of all the elements in the rows the sets in the columns, and a "1'" in position (i,j) if element i is in set j. vennCounts is meant to be used with decideTests. --Naomi At 02:15 AM 7/15/2009, amit mandal wrote: >hello amrit, > You can make Venn diagram in R using the function 'vennCounts' in the >"limma" package (for microarray data analysis). > I haven't used the function so unable to give you any worked out example. >Nevertheless, if you are in a jiffy then you visit - > http://bioinfogp.cnb.csic.es/tools/venny/index.html > >Online venn diagram utility and works good. Since presently the gene list is >small, you can as well use this. > > >cheers.. >amit > >On Wed, Jul 15, 2009 at 9:56 AM, amrit karki <akarki001 at="" yahoo.com=""> wrote: > > > Dear Ting-Yuan > > Thank you so much for your help. I still have one > > more question for you. I am trying to construct venn diagram in > > r-programming but could not success. For example: i have 100 genes in > > set A only, 50 genes in set B only and there are 25 common genes in > > both set (in intersection). So, would you mind to suggest how it is > > possible to construct venn diagram in r-programming. > > Thank you. > > With best regards. > > Amrit Karki > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > >-- >--------------------------------------------------------------- >The robbed that smiles, steals something >from the thief. >- Shakespeare >--------------------------------------------------------------- > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

hello amrit, You can make Venn diagram in R using the function 'vennCounts' in the "limma" package (for microarray data analysis). I haven't used the function so unable to give you any worked out example. Nevertheless, if you are in a jiffy then you visit - http://bioinfogp.cnb.csic.es/tools/venny/index.html Online venn diagram utility and works good. Since presently the gene list is small, you can as well use this. cheers.. amit On Wed, Jul 15, 2009 at 9:56 AM, amrit karki <akarki001@yahoo.com> wrote: > Dear Ting-Yuan > Thank you so much for your help. I still have one > more question for you. I am trying to construct venn diagram in > r-programming but could not success. For example: i have 100 genes in > set A only, 50 genes in set B only and there are 25 common genes in > both set (in intersection). So, would you mind to suggest how it is > possible to construct venn diagram in r-programming. > Thank you. > With best regards. > Amrit Karki > > > > [[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 > -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]