R help - Oct 2007 - Compute R2 and Q2 in PLS with pls.pcr package

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 Investigaci?n Pr?ncipe Felipe

Avda. Autopista Saler 16

46013 Valencia Spain

http://bioinfo.cipf.es

==========================================
CAMDA2007 Conference @ CIPF

http://camda.bioinfo.cipf.es

Ana Conesa wrote:
> I am using the mvr function of the package pls.pcr to compute PLS 
> resgression
You should consider switching to the package 'pls'.  It supersedes
'pls.pcr', which is no longer maintained (the last version came in
2005).

In pls, you would do the following to get R^2 and cross-validated R^2
(A.K.A. Q^2):

mypls <- plsr(Ytrain ~ Xtrain, ncomp = 1, validation="LOO")
## R^2:
R2(mypls, estimate = "train")
## cross-validated R^2:
R2(mypls)
## Both:
R2(mypls, estimate = "all")

-- 
Bj?rn-Helge Mevik