Displaying 5 results from an estimated 5 matches for "bhpls1".
2011 May 17
1
Help with PLSR with jack knife
...arious 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(BHPL...
2011 May 17
1
help with PLSR Loadings
Hi
When I call for the loadings of my plsr using the command,
x <- loadings(BHPLS1)
my loadings contain variable names rather than numbers.
>str(x)
loadings [1:94727, 1:10] -0.00113 -0.03001 -0.00059 -0.00734 -0.02969 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:94727] "PCIList1" "PCIList2" "PCIList3" "PCIList4" ......
2011 May 18
1
Help with Memory Problems (cannot allocate vector of size)
While doing pls I found the following problem
> BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, data = PLSdata, jackknife =
>FALSE, validation = "LOO")
when not enabling jackknife the command works fine, but when trying to enable
jackknife i get the following error.
>BHPLS1 <- plsr(GroupingList ~ PCIList, ncomp = 10, dat...
2011 May 12
1
Fw: Help with PLSR
...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 fo...
2011 Jun 08
1
Help with plotting plsr loadings
Hi
I am attempting to do a loadings plot from a plsr object. I have managed to do
this using the gasoline data that comes with the pls package. However when I
conduct this on my dataset i get the following error message.
>plot(BHPLS1, "loadings", comps = 1:2, legendpos = "topleft", labels = "numbers",
>xlab = "nm")
Error in loadingplot.default(x, ...) :
Could not convert variable names to numbers.
str(BHPLS1_Loadings)
loadings [1:8892, 1:60] -0.00717 0.00414 0.02611 0.00468 -0...