

Hi 
I am attempting to use plsr which is part of the pls package in r. I 
amconducting analysis on datasets to  identify which proteins/peptides are 
responsible for the variance between sample groups (Biomarker Spoting) in a 
multivariate fashion. 


I have a dataset in R called "FullDataListTrans". as you can see below the 
structure of the data is 40 different rows representing a sample and 94,272 
columns each representing a peptide.

>str(FullDataListTrans)
 num [1:40, 1:94727] 42 40.9 65 56 61.7 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:40] "X" "X.1" "X.12" "X.13" ...
  ..$ : NULL

I have also created a vector "GroupingList" which gives the groupnames for each 
respective sample(row).

> GroupingList
 [1] 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4
[39] 4 4
> str(GroupingList)
 int [1:40] 1 1 1 1 1 1 1 1 1 1 ...

I am now stuck while conducting the plsr. I have tried various methods of 
creating structured lists etc  and have got nowhere. I have also tried many 
incarnations of 


BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = FeaturePresenceExpected[1], data 
= FullDataListTrans, validation = "LOO")

Where am I going wrong. Also what is the easiest method to identify which of the 
94,000 peptides are most important to the variance between groups.

Thanks in advance for any help

Amit Patel
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