Hi Bryan,
Many thanks for the replies. The data is gene expression data for 36 samples over 11k genes. I see that I can plot PC1 vs PC2 by using $x, but compared to biplot() I can see that the range of values are different. For example, if I use plot() the PC1 scale ranges from -150 to 150 whereas in biplot() it scales from -0.4 to 0.4. Do you know what scaling biplot() uses? Does it even matter? Cheers, Chris On 07/05/2012 14:36, "Bryan Hanson" <han...@depauw.edu> wrote: >Christian, is that 36 samples x 11K variables? Sounds like it. Is this >spectroscopic data? > >In any case, the scores are in the list element $x as follows: > >answer <- prcomp(your matrix) > >answer$x contains the scores, so if you want to plot the 1st 2 pcs, you >could do > >plot(answer$x[,1], answer$x[,2]) > >Because the columns of answer$x contain the scores of the PCs in order. > >[I see Jessica just answered...] > >If you want the loading plot, it's going to be interesting with all those >variables, but this will do it: > >plot(1:11000, answer$rotation[,1], type = "l") # for the loadings of the >1st PC > >Depending upon what kind of data this is, the 1:11000 could be replaced >by something more sensible. If it is spectroscopic data, then replace it >with your frequency values. > >By the way, plot(answer) will give you the scree plot to determine how >many PCs are worthy. > >Good luck. Bryan > >*********** >Bryan Hanson >Professor of Chemistry & Biochemistry >DePauw University > >On May 7, 2012, at 6:22 AM, Christian Cole wrote: > >> I have a decent sized matrix (36 x 11,000) that I have preformed a PCA >>on >> with prcomp(), but due to the large number of variables I can't plot the >> result with biplot(). How else can I plot the PCA output? >> >> I tried posting this before, but got no responses so I'm trying again. >> Surely this is a common problem, but I can't find a solution with >>google? >> >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >>http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > The University of Dundee is a registered Scottish Charity, No: SC015096 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.