Question: PLMset and image function
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gravatar for Edwards.Stephen@epamail.epa.gov
12.8 years ago by
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ADD COMMENTlink modified 12.8 years ago by Seth Falcon7.4k • written 12.8 years ago by Edwards.Stephen@epamail.epa.gov50
Answer: PLMset and image function
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gravatar for Seth Falcon
12.8 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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
ADD COMMENTlink written 12.8 years ago by Seth Falcon7.4k
Answer: PLMset and image function
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gravatar for Alvord, Greg DMS [Contr]
12.8 years ago by
Alvord, Greg DMS [Contr]160 wrote:
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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 12.8 years ago by Alvord, Greg DMS [Contr]160
Answer: PLMset and image function
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gravatar for James W. MacDonald
12.8 years ago by
United States
James W. MacDonald52k wrote:
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.
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ADD REPLYlink written 12.8 years ago by Edwards.Stephen@epamail.epa.gov50
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.
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