search for: spectra

Dear R users, I am a newbie. Just switched from MATLAB. So thanks a lot for your patience. I have 50000 spectra collected in field. Each spectra has two columns : Wavelength (56) and the actual measurement. Each measurement came in a different .txt file on disk (50000 files in total). I wrote a script that reads every spectra in a for loop and constructs two variables : Wavelength (56) and Reflectance (5...

Hi, I'm trying to match peaks between chromatographic runs. I'm able to match peaks when they are chromatographed with the same method, but not when there are different methods are used and spectra comes in to play. While searching I found the ALS package which should be usefull for my application, but I couldn't figure it out. I made some dummy chroms with R, which mimic my actual datasets, to play with, but after looking at the manuals of ALS, I'm affraid I can't get the job d...

Hi all, I need to insert the name of spectra in a stacked plot obtained with hyperspec. I use this command plot(spectra [c(-1:-4, -6:-8, -10:-12, -14:-16)], stacked = T) but, in this way R draw nameless spectra on the Y axis. How can I solve the problem? Thank you for any suggestion. Best regards, Roberto -- View this message in conte...

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 s...

I would really appreciate it if someone can give suggestions on how to do spectra fitting in R using ordinary least square fitting and non-negativity constraints. The lm() function works well for ordinary least square fitting, but how to specify non-negativity constraints? It wouldn't make sense if the fitting coefficients coming out as negative in absorption spectra deconvo...

Hi I'm trying to write a generic script for processing some data which finishes off with some plots. Given Im never sure how many columns will be in my dataframe I wanted to using the following plot(spectra.wavelength, cormat, type = "l", ylim=c(-1,1), xlab="Wavelength (nm)", ylab="Correlation") however even if I specify as type="l" it appears plot as points (right hand plot). If I specify a range such as plot(650:700, cormat, type = "l", ylim=c(-1,...

...ta : T=read.table('bladder bis concatenation colonne.txt',header=TRUE) spec=new("hyperSpec",wavelength=T[,1],spc=t(T[,-1]),data=data.frame(sample=colnames(T[,-1])),label=list(.wavelength="Raman shift (cm-1)",spc="Intensity (a.u.)")) #baseline correction of the spectra spec=spec[,,500~1800] bl=spc.fit.poly.below(spec) spec=spec-bl #normalization of the spectra spec=sweep(spec,1,apply(spec,1,mean),'/') #PCA pca=prcomp(~ spc,data=spec$.,center=TRUE) scores=decomposition(spec,pca$x,label.wavelength="PC",label.spc="score/a.u.") loadings=...

Hello, I'm still a newbie user and struggling to automate some analyses from SigmaPlot using R. R is a great help for me so far! But the following problem makes me go nuts. I have two spectra, both have to be fitted to reference data. Problem: the both spectra are connected in some way: the stoichiometry of coefficients "cytf.v"/"cytb.v" is 1/2. {{In the SigmaPlot workflow one has to copy the two spectra into one column beneath each other and the two spectra are som...

Hi, I have a data frame Y with the following information, ORF spectra 1 YAL001C 2 2 YAL005C 21 3 YAL007C 2 4 YAL012W 8 5 YAL016W 24 6 YAL019W 3 7 YAL020C 2 8 YAL021C 7 9 YAL022C 3 10 YAL023C 6 11 YAL026C 2 12 YAL029C 1 13 YAL031C 1 14 YAL035W 48 15 YAL038W 173 16 YAL041W 4 17 YAL...

Dear all, This is potentially a bug in spec.pgram, when the number of samples is odd,spec.pgramreturns a different result withfast = TRUE, the example below contains the two varieties with a reference spectrum calculated manually. the number of returned spectra is also larger (50 compared to 49) whenfast = TRUE x <- rnorm( 99 ) plot(spec.pgram(x, taper = 0 , detrend = FALSE , plot = FALSE , fast = FALSE )$spec, ty = 'l' ) lines(spec.pgram(x, taper = 0 , detrend = FALSE ,plot = FALSE , fast = TRUE )$spec, col = 'red'...

Hi I'm fairly new to R and am trying to analyse some large spectral datasets using stepwise regression (fairly standard in this area). I have a field sampled dataset, of which a proportion has been held back for validation. I gather than step() needs to be fed a regression model and lm() can produce a multiple regression. I had thought something like: spectra.lm...

Hi all, I'll have to filter Raman spectra and I would like to do so in R. I'm trying to figure out how. Maybe one of you could help me ... This is what I have to do: General: separate the real spectrum (the set of peaks) from two contaminations: a drifting background and (white) noise Constraints (which should help the task): A -...

Dear R-helpers, I'm working on mass spectra in randomForest/R, and following the recommendations for the case of noisy variables, I don't want to use the default mtry (sqrt of nvariables), but I'm not sure up to which proportion mtry/nvariables it makes sense to increase mtry without "overtuning" RF. Let me tell my exam...

look at the spectrums before you do the cbind - I would not suggest letting R wrap the data to fill in a data frame. I would suggest using something that you "know how it acts" in the frequency domain like zero. You are probably introducing periodicies that are not real, and I would suggest not to go down this path. As for finding commonalities amongst signals- it all depends on what

I am reading some documentation about Cross Spectrum Analysis as a technique to compare spectra. My understanding is that it estimates the correlation strength between quasi-periodic structures embedded in two signals. I believe it may be useful for my signals analysis. I was referred to the R functions that implement this type of analysis. I tried all the examples which generated a seri...

Dear collegues, I´ ve worked with near infrared (NIR) spectroscopy to assess chemical, physical, mechanical and anatomical properties of wood. I use "The Unscrambler" software to correlate the matrix of dependent variables (Y) with the matrix of spectral data (X) and I would like to migrate to R. The matrix of spectral variables is very large (2345 columns and n lines, where n = samples), so we used Partial Least Squares Regression to predict a variable y (content of cellulose, for instance) based on the spectral variables, which are the NIR wavel...

Hi there, I hope to draw a plot like this: http://www.sg-chem.net/swizard/Ru-bqdi-spectra.gif is it possible to draw it using R? thanks for any suggestions. regards, Jinsong

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi I have 10.000 simulations for a sensitivity analysis. I have done a few sensitivity analysis for different response variables already, but now, as most of the simulations (if not all) show some cyclic behaviour, see how the independent input parameter influence the frequency of the cyclic changes and "how cyclic" they actually are. So

Hi everyone, I am working on analyzing spectra which requires hundreds of kruskal wallis tests to be performed. Once significant results are found post tests are performed ect. My questions are: how do I perform all these kw tests and save just the pvalues in a table? Is there anyway to have R automatically perform post tests if a result of...

hello all, for my diploma-thesis i want to statitically analyze near-infrared-spectra. a spectrum is given by the y-values of 1038 equi-distant x-points. in nature, a spectrum is a continuous curve. for analysis, every x-point is seen as a statistical variable. now my problem: first, i read a csv-table in a data.frame called sTable via read.table. besides some meta-data there are...