Message-ID: <OF0C611D67.53457FAD-ONC1256D17.00479094-C1256D17.0047D0E2@tomware.it>
Date: 2003-04-29T13:13:39Z
From: alessandro.semeria@cramont.it
Subject: plot(pam.object) error with R-1.7.0 on Red-Hat 8.0 i686
Hello Martin!
Here the script to create mel.data from data set freely
available attached to"Molecular Classification
of Cutaneous Malignant Melanoma
by Gene Expression Profiling" (Bittner et al., 2000):
(melanoma.csv is an ASCII comma separeted containing data and
with first raw= conditions names)
library(mva)
cond<- scan(file="melanoma.csv",what=character(38), sep=",",nlines=1)
mel<- matrix(scan("melanoma.csv",sep=",",skip=1),ncol=38,byrow=T)
dim(mel)
mel.bittner <- mel[1:3613,1:31]
cond.bittner <- cond[1:31]
mel.bittner[mel.bittner<0.02] <- 0.02
mel.bittner[mel.bittner>50] <- 50
mel.bittner <- log2(mel.bittner)
mel.bittner.median <- apply(mel.bittner,2,median)
mel.bittner.mean <- apply(mel.bittner,2,mean)
mel.bittner.sd <- apply(mel.bittner,2,sd)
mel.data <- sweep(data.matrix(mel.bittner),2,mel.bittner.median)
Thanks!
A.S.
----------------------------
Alessandro Semeria
Models and Simulations Laboratory
The Environment Research Center - Montecatini (Edison Group),
Via Ciro Menotti 48,
48023 Marina di Ravenna (RA), Italy
Tel. +39 544 536811
Fax. +39 544 538663
E-mail: asemeria at cramont.it