Hi Jessica,
THanks for pointing that out. The scaling in biplot() doesn't seem to make sense to me, however. The default value for scale=1 therefore lambda ^ (1-scale) -> lambda ^ 0 which is 1 regardless of what lambda is. Which can't be right? Anyway, I won't worry about it anymore as you and Bryan have confirmed that I am doing the right thing by plotting the $x data and will ignore biplot(). Many thanks, Chris On 07/05/2012 15:25, "Jessica Streicher" <j.streic...@micromata.de> wrote: >And i always forget the question.. > >I haven't understood biplots a 100%, but from what i gleaned this scaling >is done so it looks better/is easier to read, while the scaling retains >certain properties of the biplot (something about projecting). > >If you want to use the data for anything else, i wouldn't use that >scaling, just use what the prcomp() or princomp() function returns to you. > > >Am 07.05.2012 um 16:11 schrieb Jessica Streicher: > >> Biplot, depending on what parameters you give it, scales the data in a >>certain way. >> >> See >>http://stat.ethz.ch/R-manual/R-patched/library/stats/html/biplot.princomp >>.html >> >> scale >> The variables are scaled by lambda ^ scale and the observations are >>scaled by lambda ^ (1-scale) where lambda are the singular values as >>computed by princomp. Normally 0 <= scale <= 1, and a warning will be >>issued if the specified scale is outside this range. >> >> >> >> Am 07.05.2012 um 16:01 schrieb Christian Cole: >> >>> Hi Jessica, >>> >>> Yes, that does help. It confirms my digging around in the prcomp >>>object. >>> >>> I was plotting $x, but wasn't sure whether this was appropriate. Mainly >>> because the data ranges are different in $x than when plotted by >>>biplot() >>> - as I mentioned my reply to Bryan. Do you know if this difference is >>>data >>> range matters? >>> Many thanks, >>> >>> Chris >>> >>> >>> >>> On 07/05/2012 14:24, "Jessica Streicher" <j.streic...@micromata.de> >>>wrote: >>> >>>> That depends on what you want to plot there. Basically, you could just >>>> use plot() with pcaResult$x. You might need to define which PCs you >>>>want >>>> to plot there though. >>>> >>>> pcaResult<-prcomp(iris[,1:4]) >>>> plot(pcaResult$x) # gives the first 2 PCs >>>> plot(pcaResult$x[,2:3]) #gives the second vs the 3rd PC >>>> >>>> or if you want to see more you can use pairs() >>>> >>>> pairs(pcaResult$x) >>>> >>>> if you want things colored, theres the col parameter that works for >>>>both >>>> functions: >>>> >>>> pairs(pcaResult$x,col=iris[,5]) >>>> >>>> Does this help? >>>> >>>> Am 07.05.2012 um 12:22 schrieb Christian Cole: >>>> >>>>> 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. >>>> >>>> ______________________________________________ >>>> 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 >>> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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. > >______________________________________________ >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.
