[R] Help with PLSR with jack knife

From: Amit Patel <amitrhelp_at_yahoo.co.uk>
Date: Tue, 17 May 2011 17:10:53 +0100 (BST)


Hi

I am analysing a dataset of 40 samples each with 90,000 intensity measures for various peptides. I am trying to identify the Biomarkers (i.e. most significant peptides). I beleive that PLS with jack knifing, or alternativeley CMV(cross-model-validation) are multivariateThe 40 samples belong to four different groups.

I have managed to conduct the plsr using the commands:

BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, validation =
"LOO")
and

BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, validation =
"CV")

I have also used the following command to obtain the loadings

BHPLS1_Loadings <- loadings(BHPLS1)

Now I am unsure of how to utilise these to identify the significant variables. Do I need to use any loops?

str(BHPLS1_Loadings)
 loadings [1:94727, 1:10] -0.00113 -0.03001 -0.00059 -0.00734 -0.02969 ...

Many thanks in advance
AK

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