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
Suggestions: Terminology & Pkgs for following spectra over time
3 messages · Bryan Hanson, Baptiste Auguie, Katharine Mullen
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 at 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 Augui? 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
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 at 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.