hi Deepak, This is a general R question as it doesn't involve software from Bioconductor, so you should post future questions like this to the R help mailing list https://stat.ethz.ch/mailman/listinfo/r-help or as an R tagged question on stackoverflow http://stackoverflow.com/questions/tagged/r. You can obtain the mean for each group many ways. One way is to use the ddply function in the plyr package on CRAN: http://cran.r-project.org/web/packages/plyr/plyr.pdf d = data.frame(PC1 = pc$x[,1], PC2 = pc$x[,2], f = factor(condition)) library(plyr) groupmeans = ddply(d, "f", summarise, mPC1=mean(PC1), mPC2=mean(PC2)) This gives the mean of PC1 and the mean of PC2 for each group. Mike On Tue, Jul 22, 2014 at 5:10 AM, deepak karthik <deepaksrna at="" gmail.com=""> wrote: > Hi Michael > > Even if i perform coloring the carcinoma it is so crowded , > i am not able to distinguish between cancer . That is the reason that i > wanted to find a way to point out a single point for each cancer . My > ultimate is to find the cancer which are related , with respective my gene > of interest . Please suggest me a better approach. > > thank you, > Deepak > > > > On Wed, Jul 16, 2014 at 3:50 PM, Michael Love <michaelisaiahlove at="" gmail.com=""> > wrote: >> >> hi Deepak, >> >> We like to always keep the discussion on the list, to avoid having to >> answer duplicate questions. >> >> Collapsing all the patients into a single point defeats the purpose of >> PCA: to see the distances between individual samples and groups of >> samples. Showing just the mean for each group might mislead someone >> looking at the plot into thinking the clusters are distinct, when the >> samples might have high variance around that average point. I would >> recommend instead just coloring the types of carcinoma. >> >> Mike >> >> On Wed, Jul 16, 2014 at 5:43 AM, deepak karthik <deepaksrna at="" gmail.com=""> >> wrote: >> > Thanks for your reply. >> > I have data of hundreds of patients from each carcinoma , consisting of >> > rnaseq expression with certain gene of interest. If i perform pca >> > analysis >> > for numerous carcinoma , my pca plot would be clumsy difficult to find >> > out >> > the type of carcinoma are clustered together . so i would like to mark >> > single point for a particular type of carcinoma with consideration of >> > my >> > rnaseq expression for my gene of my interest . Thanks in advance . >> > >> > with regards, >> > S.Deepak >> > >> > >> > On Tue, Jul 15, 2014 at 9:31 PM, Michael Love >> > <michaelisaiahlove at="" gmail.com=""> >> > wrote: >> >> >> >> You might get more feedback if you describe what kind of experiment >> >> you have performed (microarray or RNA-Seq?). >> >> >> >> The other reason you might not be getting response is that the >> >> principal component functions are not implemented in Bioconductor, but >> >> in base R. So it's not necessarily a Bioconductor question, but a >> >> statistics/R question. >> >> >> >> The very basic code for making a PCA plot from an expression set 'e' >> >> would >> >> be >> >> >> >> pc = prcomp( t ( exprs( e ) ) ) >> >> plot( pc$x[ , 1:2 ] ) >> >> >> >> On Tue, Jul 15, 2014 at 8:36 AM, karthik [guest] >> >> <guest at="" bioconductor.org=""> >> >> wrote: >> >> > Hi all, >> >> > >> >> > I am writing this mail for second time. I wanted perform a >> >> > pca >> >> > analysis ,for each cancer type and genes of interest expression. I >> >> > just >> >> > wanted to plot only a single point which is able represent each >> >> > cancer and >> >> > their genes expression .Can you please explain me on it.( And cancer >> >> > per >> >> > gene basis should i take median or mean values to represent their >> >> > expression). Thanks in advance. >> >> > >> >> > >> >> > -- output of sessionInfo(): >> >> > >> >> > pca() >> >> > >> >> > -- >> >> > Sent via the guest posting facility at bioconductor.org. >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > >> > >> > -- >> > >> > Deepak karthik >> > >> > PhD student >> > >> > +972-054-5683140 >> > >> > >> > Dr. Mali Salmon-Divon, Genomic Bioinformatics laboratory >> > >> > The Department of Molecular Biology >> > >> > Ariel University, Israel > > > > > -- > > Deepak karthik > > PhD student > > +972-054-5683140 > > > Dr. Mali Salmon-Divon, Genomic Bioinformatics laboratory > > The Department of Molecular Biology > > Ariel University, Israel