[BioC] PLMset and image function

[Alvord, Greg (DMS) [Contr]]

Hi Steve - I'm a newbie with Bioconductor and R.  I am currently running
R version 2.4.0 abnd BioConductor version 1.9, under Windows.  I ran
your commands on the Dilution data set and was able to get the image
plot without any trouble.  I did not receive any error indicating that
the 'argument must be matrix-like'.   Perhaps there is some instability
in R version 2.5.0.

Greg
 
W. Gregory Alvord, Ph.D.
Director, Statistical Consulting Services
Computer and Statistical Services
National Cancer Institute at Frederick
Post Office Box B 
Frederick, MD 21702-1201
Phone: 301.846.5101
Facsimile: 301.846.6196
E-Mail gwa at css.ncifcrf.gov


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
Edwards.Stephen at epamail.epa.gov
Sent: Tuesday, March 13, 2007 10:38 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] PLMset and image function

This may be a known issue, but I'm trying to use the image function with

PLMset objects in R2.5 and get the following error:  argument must be 
matrix-like.

> data(Dilution)
> Pset1 <- fitPLM(Dilution)
> image(Pset1, type = "weights", which = 3)
Error in image.default(Pset1, type = "weights", which = 3) : 
        argument must be matrix-like
> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-26 r40806) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
ENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils" 
[7] "datasets"  "methods"   "base" 

other attached packages:
    simpleaffy     genefilter       survival    hgu95av2cdf
hgu133plus2cdf 

       "2.9.3"       "1.13.8"         "2.31"       "1.15.0"
"1.15.0" 

       affyPLM          gcrma    matchprobes       affydata
affy 

     "1.11.13"        "2.7.1"        "1.7.4"       "1.11.1"
"1.13.14" 

        affyio        Biobase 
       "1.3.3"      "1.13.39" 

Steve

----------------------------------------
Stephen W. Edwards, Ph.D.
Systems Biologist, ADHIO, NHEERL, ORD, USEPA
U.S. Environmental Protection Agency (B305-01)
109 TW Alexander Drive
Research Triangle Park, NC  27711
Ph#: 919/541-0514       FAX#: 919/685-3221



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