PAM implements the Nearest Shrunken Centroid method of Tibshirani, Hastie, Narasimhan and Chu (May 14, 2002) described in Diagnosis of multiple cancer types by shrunken centroids of gene expression.
Note that there are a number of steps in the installation but all are
simple and steps 1-4 need to be done only once. They involve
installation of the R package, and the pamr
package, both of
which are used by PAM for Excel.
After these steps, PAM can be used from within your version of Excel.
This document describes the installation and use of the PAM for R package. This document is always kept up-to-date at The PAM Page.
Follow the instructions. Click on
CRAN under
Download. Pick a mirror closest to you. You probably want a
pre-compiled version. For windows, choose the
Windows (95 or later) link, select base
, and download SetupR.exe
.
Installation takes 5-10 minutes.
R is a great package, and is worth knowing about!
pamr
from the
PAM for R Website. Note that PAM for Excel and PAM
for R are matched packages and one should therefore make sure that
same versions of both packages are installed, for example, version
1.12. When you download the R package, most browsers offer you a
choice of opening the file or saving it. Elect to save it and remember
the name of the folder where you saved it.
Double click on the R icon on your desktop, pull down the
Packages
menu item and select
Install packages from local zip file
. A file chooser dialog will
allow you to select the file
pamr_1012.zip
that you just saved in the previous step.
Add/Remove Programs
in your
control panel, before installing the newer version.
Go to the
PAM for Excel Registration page and then follow instructions
to download the pam_1012.zip
file. Unzip it and click on the
Setup
icon to install it.
Tools
menu and choose Addin
.
Browse to find the Addin file that the installation in the previous
step installed. Unless you changed the default on installation, it is
usually placed in the directory
C:\Program files\PAMVB\Addin\pam.xla
Click OK
, and now you should see a PAM
and PAM
controller
button on the top of your Excel window. You might have SAM
installed already- that's OK! They can co-exist in your Excel.
The data setup for PAM is much like that for SAM. There is one line per gene. There are additional rows at the top of the spreadsheet for class labels and (optional) sample and batch labels. Example files have been provided for you. For example the file
C:\Program Files\PAMVB\Examples\khan.xls
Load up this example, click on the PAM
button and you should see
a PAM Dialog
. Specify the following inputs:
Click OK
to start the PAM analysis.
A detailed manual for PAM is available in the directory
C:\Program Files\PAMVB\doc\pam.pdf
It also contains the above installation instructions and a lot more detail. Any serious user of PAM should refer to it.