NIT: Fatty acids study in R – Part 005

March 9, 2012
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(This article was first published on NIR-Quimiometría, and kindly contributed to R-bloggers)

There are several algorithms to run a PLS regression (I recommend to consult the books: “Introduction to Multivariate Analysis in Chemometrics - Kurt Varmuza & Peter Filzmozer” and “Chemometrics with R – Ron Wehrens”).
We are going to use the PLS package, and we are going to develop, maybe the constituent which looks more promising: Oleic Acic (C18:1).
Of course we are going to use the MSC pretreatment. For vcross validation we are going to use “leave one out”.I decide a maximum of 16 PLS terms.
> C18_1<- plsr(C18_1~NITmsc, ncomp = 16,data =fattyac_msc, 
  + validation = "LOO")
Allways is good to look to the plots:
>  plot(C18_1,ncomp=12,which="validation")
We can see how from Term 12 the RMSEP increase.
We can see in the XY plot, how we have a few samples with a high residual (probably wrong lab value for one or two of them). We can delete these samples from the data set to develop the equation again (RMSEP will decrease a little bit and the RSQ will increase)
We have to consider the Lab error for this parameter of the reference method: Chromatography.
The extreme sample 66, fits well in the model, so we decide to keep it. The model seems quite good to predict “Oleic acid”.  We will test it in a near future with new samples (independent test set).

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