On Mon, Apr 23, 2012 at 12:01 AM, Michael <comtech....@gmail.com> wrote: > yes, but that is not a good Review or Survey... thx
But the packages listed there do have their own documentation and vignettes. For instance the rrcov package seems to have a nice vignette about its design as well as methods it implements, and references to these methods for further reading: http://cran.r-project.org/web/packages/rrcov/vignettes/rrcov.pdf You'll see at least a few mentions of PCA, which will lead you to other package/papers/etc. Enjoy, -steve > > On Sun, Apr 22, 2012 at 9:47 PM, Bert Gunter <gunter.ber...@gene.com> wrote: > >> As I believe I already told you, look at the CRAN Robust task view. >> >> -- Bert >> >> On Sun, Apr 22, 2012 at 6:29 PM, Michael <comtech....@gmail.com> wrote: >> > Even in R, there are so many of "robust PCA"... any survey or review of >> all >> > these different methods? >> > >> > On Sun, Apr 22, 2012 at 6:58 PM, Joshua Wiley <jwiley.ps...@gmail.com >> >wrote: >> > >> >> On Sun, Apr 22, 2012 at 4:43 PM, Michael <comtech....@gmail.com> wrote: >> >> > I actually tried "robustPca" in "pcaMethods" on bioconductor. >> >> > >> >> > It keeps giving me the warning "Input data is not complete"... >> >> > >> >> > Reading into the function: >> >> > >> >> > When there is no "NA"s, it will give this warning... >> >> > >> >> > It seems that there is a bug in this code... >> >> > >> >> > Is it reliable at all? >> >> > >> >> > --------------------- >> >> > >> >> > >> >> >> robustPcafunction (Matrix, nPcs = 2, verbose = interactive(), ...) >> >> > { >> >> > nas <- is.na(Matrix) >> >> > if (!any(nas) & verbose) { >> >> > cat("Input data is not complete.\n") >> >> > cat("Scores, R2 and R2cum may be inaccurate, handle with >> care\n") >> >> > } >> >> >> >> that seems to issue the notes when there are *not any missing* and >> >> verbose is TRUE. I would submit a bug report to the author. >> >> >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > On Fri, Apr 20, 2012 at 9:58 AM, Kevin Wright <kw.s...@gmail.com> >> wrote: >> >> > >> >> >> You can also have a look at the pcaMethods package on Bioconductor. >> >> >> >> >> >> Kevin >> >> >> >> >> >> >> >> >> On Thu, Apr 19, 2012 at 11:20 PM, Michael <comtech....@gmail.com> >> >> wrote: >> >> >> >> >> >>> Hi all, >> >> >>> >> >> >>> I found that the PCA gave chaotic results when there are big changes >> >> in a >> >> >>> few data points. >> >> >>> >> >> >>> Are there "improved" versions of PCA in R that can help with this >> >> problem? >> >> >>> >> >> >>> Please give me some pointers... >> >> >>> >> >> >>> Thank you! >> >> >>> >> >> >>> [[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< >> http://www.r-project.org/posting-guide.html> >> >> <http://www.r-project.org/posting-guide.html> >> >> >>> and provide commented, minimal, self-contained, reproducible code. >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Kevin Wright >> >> >> >> >> >> >> >> > >> >> > [[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< >> http://www.r-project.org/posting-guide.html> >> >> > and provide commented, minimal, self-contained, reproducible code. >> >> >> >> >> >> >> >> -- >> >> Joshua Wiley >> >> Ph.D. Student, Health Psychology >> >> Programmer Analyst II, Statistical Consulting Group >> >> University of California, Los Angeles >> >> https://joshuawiley.com/ >> >> >> > >> > [[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. >> >> >> >> -- >> >> Bert Gunter >> Genentech Nonclinical Biostatistics >> >> Internal Contact Info: >> Phone: 467-7374 >> Website: >> >> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm >> > > [[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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ______________________________________________ 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.