R help - May 2011 - Fw: Help with PLSR

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
	[[alternative HTML version deleted]]

Amit Patel <amitrhelp at yahoo.co.uk> writes:
>>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.
You are not telling us what happens (or how you tried to make
"structured lists"), but from your description of the
data, FullDataListTrans is a matrix with only the the predictor
variables, and GroupingList is a vector with the response.  The data
argument of plsr() (as of most modelling functions in R) expects a
data.frame with both response and predictor variables.

Try this:

mydata <- data.frame(GroupingList = GroupingList, PCIList =
I(FullDataListTrans))

(The I() is to prevent R from making the coloumns in FullDataListTrans
separate variables in the data frame.)

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

-- 
Regards,
Bj?rn-Helge Mevik