[R] Need Help with robustbase package: fitnorm2 and plotnorm2

From: M. Jankowski <mjankowski_at_gmail.com>
Date: Fri, 08 Jun 2007 00:01:40 -0500


This is my first post requesting help to this mailing list. I am new to R. My apologies for any breach in posting etiquette. I am new to this language and just learning my way around. I am attempting to run some sample code and and am confused by the error message: Loading required package: rrcov
Error in fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor) :

        Required package rrcov could not be found. In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE,
>

that I get when I attempt to run the following sample snippet of code. The error above is taken from the code below. I am running Ubuntu Linux with all the r packages listed in the Synaptic package manager (universa). I loaded the "prada" bioconductor package as instructed in the comments and the robustbase was downloaded and installed with the command: "sudo R CMD INSTALL robustbase_0.2- 7.tar.gz", the robustbase folder is in "/usr/local/lib/R/site-library/" When I type in 'library(robustbase)' no error appears; I believe robustbase is installed correctly. The sample code was taken from FCS-prada.pdf. The sample code was written in 2005, I understand that rrcov was made part of the robustbase package sometime in the past year. This may be the cause of the problem, but, if it is, I have no idea how to fix it. Thank you in advance for helping out!

Below you will find the code that generates the error and the complete output of the code. Let me know what I can do to get up and running!

Matt

#prada Bioconductor package
#http://www.bioconductor.org/repository/devel/vignette/norm2.pdf
# To install "prada"
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("prada")

library(prada)
filepath <- system.file("extdata", "fas-Bcl2-plate323-04-04.A01", package = "pra da")
print(filepath)
sampdat <- readFCS(filepath)
fdat <- exprs(sampdat)
print(dim(fdat))
print(colnames(fdat))

plot(fdat[, "FSC-H"], fdat[, "SSC-H"], pch = 20, col = "#303030", xlab = "FSC", ylab = "SSC", main = "Scatter plot FSC vs SSC") #All of this goes as the help documentation suggests it should

# 2. Show selections for various scale factors savepar <- par(mfrow=c(2,2))

for (Scalefactor in c(1.0, 1.5, 2.0, 2.5) )   {
    # The next line gives the error I've included below.     nfit <- fitNorm2 (fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor)     plotnorm2(nfit, selection = TRUE, ellipse = TRUE,

              xlab="FSC-H", ylab="SSC-H",
              main=paste("SSC-H vs. FSC-H (ScaleFactor=",ScaleFactor,")", sep=""
))
  }
par(savepar)

Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type     'openVignette()' or start with 'help(Biobase)'. For details     on reading vignettes, see the openVignette help page.

Loading required package: RColorBrewer
Loading required package: grid
Loading required package: geneplotter
Loading required package: annotate

KernSmooth 2.22 installed
Copyright M. P. Wand 1997
[1] "/usr/local/lib/R/site-library/prada/extdata/fas-Bcl2-plate323-04-04.A01" [1] 2115 8

   $P1N $P2N $P3N $P4N $P5N $P6N $P7N $P8N "FSC-H" "SSC-H" "FL1-H" "FL2-H" "FL3-H" "FL2-A" "FL4-H" "Time" Loading required package: rrcov
Error in fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor) :

        Required package rrcov could not be found. In addition: Warning message:
there is no package called 'rrcov' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE,
>



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