Off topic for this list. Post on stats.stackexchange.com or similar for statistics questions.
Post on Bioconductor list for biology-related (e.g. proteomics) data anaysis questions. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jan 18, 2017 at 10:35 AM, Josh Mitteldorf <agingadv...@gmail.com> wrote: > I'm working with proteomic data, helping a student who knows biology and > has done analysis in R without understanding it in depth. > > We have 3000 protein levels for 6 ages. I can treat this as 6 vectors in > 3000-dimensional space, diagonalize a 6x6 covariance matrix and find 5 > principal components, one zero eigenvalue. My student has worked with R in > "Q mode" and he enters the transposed matrix as 3000 vectors in > 6-dimensional space. In just a few seconds, R diagonalizes a 3000x3000 > matrix! I can't imagine what that means, to diagonalize a 3000x3000 > matrix. But, of course, there are only 5 degrees of freedom in the data, > so only 5 of the eigenvalues are non-zero, and the other 2995 vectors are > junk. > > Questions: a) Is there a relationship between the principal components > of the 3000*6 matrix and the principal components of the transposed 6*3000 > matrix? > b) Is there a way to find the 5 meaningful > eigenvectors without carrying the baggage of diagonalizing the huge > 3000-dimensional matrix? > c) The big question is which version to analyze and > publish? My student tells me the transposed matrix is the common > procedure. The two yield very different-looking plots. > > Thanks for your help. > - Josh Mitteldorf > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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.