Hi > > Jim, > > Thank you for your reply. I guess I am just not understanding what the > difference is. If I run your example using the pcmatrix<- > data.frame(Q1=sample(1:5,10,TRUE),Q2=sample(1:5,10,TRUE)) and print out > pcmatrix I get: > > Q1 Q2 > 1 98 99
Thats rather surprising. I get > pcmatrix<-data.frame(Q1=sample(1:5,10,TRUE),Q2=sample(1:5,10,TRUE)) > pcmatrix Q1 Q2 1 4 4 2 3 3 3 4 1 4 4 4 5 4 2 6.... this what I get > > Then if I mirror my input file to be, would would be what the samples > from above would have created, it would look like this: > > ID,Q1,Q2 > 1,2,3 what about include dput(head(yourfile)) to your post to let us see how it looks like. Or at least str(yourfile) Regards Petr > > And I run the script printing out pcmatrix I get the exact same thing. > > Q1 Q2 > 1 98 99 > > So I would think they are basically the same representations, however > one works when passed into the prcomp function and the other does not. > I am just trying to tweak a script that we had created for us (cannot > find the guy now) so I can pass more columns of data. I clearly really > do not know what I am doing, but again thanks for you time and any > direction you can point me in would be awesome. > > Thanks > > Jason > > On Nov 1, 2012, at 3:57 AM, Jim Lemon wrote: > > > On 10/31/2012 11:47 PM, fillay89 wrote: > >> I am trying to run the R Script below, I have actually simplified it > >> to just this part that is causing issues. When I run this script I > >> continue to get an error that says "cannot rescale a constant/zero > >> column to a unit variance". I cannot figure out what is going on > >> here. I have stripped down my data file so it is more manageable so > I can try to figure this out. > >> > >> The data.txt file that is being read looks like this: > >> > >> > >> I have made this file very basic on purpose to see if I could get > >> this to work, but it is not working. Of course once I get this to > >> actually work I will expand the data file to match the data I am > actually using. > >> > >> > >> > >> If I change the attribute in the prcomp function to scale=FALSE of > >> course I can run my script. But if it is scaling...which is causing > >> the issues, it errors. > >> > >> Any help would be GREATLY appreciated. > >> > > Hi fillay89, > > You seem to be trying to run a principal component analysis on two > numbers, which won't produce anything useful. If I make up some data > that is more realistic: > > > > pcmatrix<-data.frame(Q1=sample(1:5,10,TRUE),Q2=sample(1:5,10,TRUE)) > > pcmatrix[,1] <- pcmatrix[,1] + 96 > > pcmatrix[,2] <- pcmatrix[,2] + 96 > > x.pca <- prcomp(pcmatrix,retx=TRUE,center=TRUE,scale=TRUE,cor=TRUE) > > x.pca > > Standard deviations: > > [1] 1.263267 0.635733 > > > > Rotation: > > PC1 PC2 > > Q1 0.7071068 -0.7071068 > > Q2 0.7071068 0.7071068 > > > > it runs and I get a slightly more useful result. Running your code > does bomb in exactly the way you describe, as does: > > > > x.pca <- prcomp(data.frame(Q1=99,Q2=98), retx=TRUE, center=TRUE, > > scale=TRUE, cor=TRUE) Error in prcomp.default(data.frame(Q1 = 99, Q2 > = 98), retx = TRUE, center = TRUE, : > > cannot rescale a constant/zero column to unit variance > > > > Your problem is that you have a data frame with only one value (i.e. > a constant) in each column. > > > > Jim > > ______________________________________________ > 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.
