Dear list I am using the mvr function of the package pls.pcr to compute PLS resgression using a X matrix of gene expression variables and a Y matrix of medical varaibles. I would like to obtain the R2 (sum of squares captured by the model) and Q2 (proportion of total sum of squares captured in leave-one-out cross validation) of the model. I am not sure if there are specific slots in the output of the mvr function that give these parameters (RMS and R2 parameters are given for each variable of Y). I have tried to compute it myself from the ouput of mvr but I am not sure if the values of Ypred within the validat slot are the predictions of each observation of Y when leave-one-out cross validation is applied. My code is as follows:
> mypls <- mvr(Xtrain, Ytrain, method="SIMPLS", validation="CV", ncomp=1, niter=nrow(Ytrain)) > Xhat <- mypls$training$Xscores %*% t(mypls$training$Xload) > R2 <- 1-(sum((Xhat-Xtrain)^2)/sum(Xtrain^2)) > Q2 <- 1-(sum((Ytrain-mypls$validat$Ypred[,,1])^2)/sum(Ytrain^2) Is this right? Thank you Ana ------------------------------------------- Ana Conesa, PhD Bioinformatics Department Centro de Investigación Príncipe Felipe Avda. Autopista Saler 16 46013 Valencia Spain http://bioinfo.cipf.es =========================================== CAMDA2007 Conference @ CIPF http://camda.bioinfo.cipf.es ______________________________________________ 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.
