Edwards.Stephen at epamail.epa.gov writes:
> I tried reinstalling via biocLite("affyPLM"), and I still get the
same
> error. Here is the information from traceback():
>> traceback()
> 4: stop("argument must be matrix-like")
> 3: image.default(Pset1, which = 2)
> 2: image(Pset1, which = 2)
> 1: image(Pset1, which = 2)
I'm not able to reproduce this either. The traceback suggests that
what is failing is the dispatch on affyPLM's image method.
Using a fresh R session, can you do:
library(affyPLM)
data(Dilution)
Pset1 <- fitPLM(Dilution)
showMethods("image")
selectMethod("image", signature="PLMset")
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
Center
http://bioconductor.org
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@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.UT
F-
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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Hi Stephen,
Edwards.Stephen at epamail.epa.gov wrote:
> 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
I can get this to work on both win32 and 64 bit linux with this
version
of affyPLM. You might try re-installing affyPLM. Another useful bit of
info would be a traceback() after the error (if a re-install doesn't
help).
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Edwards.Stephen at epamail.epa.gov wrote:
> I tried reinstalling via biocLite("affyPLM"), and I still get the
same
> error. Here is the information from traceback():
>
>>traceback()
>
> 4: stop("argument must be matrix-like")
> 3: image.default(Pset1, which = 2)
> 2: image(Pset1, which = 2)
> 1: image(Pset1, which = 2)
I think the problem here is you are ending up with image.default()
being
called on your PLMset instead of the image() function defined in
affyPLM, which extracts a matrix of values and then feeds that to
image.default().
What do you get if you just type Pset1 at an R prompt? Something like
this?
Probe level linear model (PLMset) object
size of arrays=640x640
cdf=HG_U95Av2 (12625 probeset ids)
number of samples=
number of probesets=12625
number of chip level parameters for each probeset= 4
annotation=hgu95av2
PLMset settings
Creating function: fitPLM
Preprocessing
Background Correction=TRUE Method= RMA.2
Normalization=TRUE Method= quantile
Model/Summarization
$constraint.type
default
"contr.treatment"
[snip]
>
> Is there a cleaner way to reinstall a package rather than simply
running
> biocLite? If so, I will try that.
That should be fine, as long as you do it using a fresh instance of R
(and no other versions opened that might have affyPLM loaded).
Best,
Jim
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
