Re: [R] Suggestions: Terminology Pkgs for following spectra over time
Hello, I've found the function isPeak from the Bioconductor package PROCess very useful for peak finding. My data was similar to yours (spectroscopy, i'm a physicist) but not time dependent. It may be a starting point to work on one spectrum, retrieve a few relevant informations (peak positions, widths, intensities,...), and process similarly at regular time intervals. www.bioconductor.org/packages/2.0/ bioc/vignettes/PROcess/inst/doc/ howtoprocess.pdf hope this helps, baptiste On 17 Apr 2008, at 02:26, Bryan Hanson wrote: Hi Folks... No code to troubleshoot here. I need some suggestions about the right terminology to use in further searching, and any suggestions about R pkgs that might be appropriate. I am in the planning stages of a project in which IR, NMR and other spectra (I'm a chemist) would be collected on various samples, and individual samples would be followed over time. The spectra will be feature rich/complex, so one can't see the changes by visual inspection. The spectra are basically 2D matrices: peaks as a function of frequencies. So the data set is in the form of spectra of a single sample over time, for multiple samples. I am wondering about methods R pkgs that can be used to analyze changes in the spectra over time. For instance, I would like to find specific peaks that are changing over time, sets of peaks that are changing in a correlated way over time etc. I'd like to do this in an efficient and statistically valid way. What I am thinking of is somewhat like a time series, somewhat like image analysis (but only 2D), but it's not quite either of those and I need to know what it's really called to investigate further. Any suggestions as to R pkgs and key words/phrases will be appreciated. TIA, Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle Indiana USA __ 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. _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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.
Re: [R] Suggestions: Terminology Pkgs for following spectra over time
Dear Bryan, For work in that general direction, look at the R News that was on 'R in chemistry' (Volume 6/3, August 2006, http://www.r-project.org/doc/Rnews/Rnews_2006-3.pdf) and the special vol. of the Journal of Statistical Software on 'Spectroscopy and Chemometrics in R' (vol 18, http://www.jstatsoft.org/v18) For ideas about modeling spectra resolved in time and frequency, the papers of Sabine van Huffel at K U Leuven may be of interest (http://www.esat.kuleuven.be/~sistawww/cgi-bin/newsearch.pl?Name=Van+Huffel+S) If you decide that you want to describe the time domain with a parametric model, then look at the package TIMP (and perhaps contact me off list). On Wed, 16 Apr 2008, Bryan Hanson wrote: Hi Folks... No code to troubleshoot here. I need some suggestions about the right terminology to use in further searching, and any suggestions about R pkgs that might be appropriate. I am in the planning stages of a project in which IR, NMR and other spectra (I'm a chemist) would be collected on various samples, and individual samples would be followed over time. The spectra will be feature rich/complex, so one can't see the changes by visual inspection. The spectra are basically 2D matrices: peaks as a function of frequencies. So the data set is in the form of spectra of a single sample over time, for multiple samples. I am wondering about methods R pkgs that can be used to analyze changes in the spectra over time. For instance, I would like to find specific peaks that are changing over time, sets of peaks that are changing in a correlated way over time etc. I'd like to do this in an efficient and statistically valid way. What I am thinking of is somewhat like a time series, somewhat like image analysis (but only 2D), but it's not quite either of those and I need to know what it's really called to investigate further. Any suggestions as to R pkgs and key words/phrases will be appreciated. TIA, Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle Indiana USA __ 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.
