Hi Chris, > I am having an issue with the OrgMassSpecR package. I run my HPLC > using a DAD detector. You are on a statistics IDE related mailing list. Have mercy with people from other fields and tell them that you are using a diode array to measure UV/VIS absorption. (And possibly let them know that you expect the absorbance A = lg I_0 - lg I ~ c.)
> My raw data is exported form chemstation as a > csv file. I then upload the csv into Rstudio no problem. Using the > DrawChromatogram function, I get a nice chromatogram, and my > retention time, peak area, and apex intensity values are given as > well. > > The problem comes with the peak area value given. The peak area is > much smaller than a value that would make sense. How do you know that (see next comment)? > My peak area value is actually less than my apex intensity value. This is not a good criterion to determine what area value would actually make sense: area and intensity have different units! Possible solution: a glance on the code in DrawChromatogram reveals that really the polygon area is calculated (as the manual specifies). Thus the area will be in counts*s or counts*min, and of course 1 count*min = 60 counts*s. How long does your analyte take to elute? Unless it is > 2 min (if time is in min) or > 2 s (for time scale in s), the numeric value of the area should be < A_max (approximating the peak as triangule). Your apex (max) absorbance should ideally be a bit below 1, so a rough guesstimate for peak area would be 1/2 A_max * Δt which will be quite below 1 if you measure time in minutes. If you detect by mass spec, you get ion counts which are large numbers, so areas are likely to be > 1 (regardless of min or s time scale). > Is this because I am> using a DAD detector rather than an MS? If so, > is there a simply way to edit the peak area equation so that it will > also work with absorbance values? Most probably you just want to get your units right! Hope that helps, Claudia PS: for future questions of this sort, you may want to consider asking on stackoverflow.com (or chemistry.stackexchange.com) where you can post nicely formatted code, calculation results and images with your question. -- Claudia Beleites Spectroscopy/Imaging Institute of Photonic Technology Albert-Einstein-Str. 9 07745 Jena Germany email: claudia.belei...@ipht-jena.de phone: +49 3641 206-133 fax: +49 2641 206-399 ______________________________________________ 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.