problem with hist.default in affystart in package affycoretools

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Kimpel, Mark W ▴ 890

@kimpel-mark-w-727

Last seen 10.3 years ago

I haven't used affycoretools since migrating to R 2.4.0 and BioC 1.9, but code that used to work has stopped working. I have tried to use affystart on two separate datasets and get the same error in hist.default. It looks to me like an affy.object is being passed as an argument to a function that does not accept it. In the code example below I have used all of the affystart defaults, but I get the same error if I supply arguments. Output, debugging info and sessionInfo are below. Thanks, Mark affystart(filenames=NULL, groups = NULL, groupnames = NULL, plot = + TRUE, pca = TRUE, squarepca = FALSE, plottype="pdf", express = c("rma"), addname = NULL, phenoData = new("phenoData")) Background correcting Normalizing Calculating Expression Error in hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) : 'x' must be numeric In addition: Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch(filenames = filenames, phenoData = phenoData) Enter a frame number, or 0 to exit 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = c("rma"), addname 2: plotHist(dat, filenames) 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) Selection: Enter an item from the menu, or 0 to exit Selection: 4 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "angle" "axes" "border" "breaks" "col" "density" "freq" "include.lowest" [9] "labels" "main" "nclass" "plot" "probability" "right" "x" "xlab" [17] "xlim" "ylab" "ylim" Browse[1]> x AffyBatch object size of arrays=834x834 features (70650 kb) cdf=Rat230_2 (31099 affyids) number of samples=13 number of genes=31099 annotation=rat2302 Browse[1]> c Enter a frame number, or 0 to exit 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = c("rma"), addname 2: plotHist(dat, filenames) 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) Selection: 0 > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" "methods" "tools" "base" other attached packages: rat2302cdf affyQCReport simpleaffy affycoretools biomaRt RCurl XML GOstats Category genefilter survival "1.14.0" "1.12.0" "2.8.0" "1.6.0" "1.8.1" "0.8-0" "1.2-0" "2.0.4" "2.0.3" "1.12.0" "2.30" KEGG RBGL annotate GO graph RWinEdt limma affy affyio Biobase "1.14.1" "1.10.0" "1.12.1" "1.14.1" "1.12.0" "1.7-5" "2.9.1" "1.12.2" "1.2.0" "1.12.2" > Mark W. Kimpel MD Official Business Address: Department of Psychiatry Indiana University School of Medicine PR M116 Institute of Psychiatric Research 791 Union Drive Indianapolis, IN 46202

GO cdf annotate affy limma RBGL simpleaffy GOstats Category affyQCReport affyio GO cdf • 1.8k views

ADD COMMENT • link updated 18.0 years ago by James W. MacDonald 67k • written 18.0 years ago by Kimpel, Mark W ▴ 890

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days ago

United States

Hi Mark, That is a weird error. It appears that hist.default() is being called on your AffyBatch object, rather than the hist() method defined in the affy package. Since you appear to have the affy package loaded, I have to assume for some reason it didn't load correctly because the method isn't getting found. If you restart R and try again, do you get the same result? You might also try just building an AffyBatch object and calling hist(abatch). If this continues, you might have a bum install of affy that may be repaired by re-installing. Best, Jim Kimpel, Mark William wrote: > I haven't used affycoretools since migrating to R 2.4.0 and BioC 1.9, > but code that used to work has stopped working. I have tried to use > affystart on two separate datasets and get the same error in > hist.default. It looks to me like an affy.object is being passed as an > argument to a function that does not accept it. In the code example > below I have used all of the affystart defaults, but I get the same > error if I supply arguments. > > Output, debugging info and sessionInfo are below. > > Thanks, > > Mark > > affystart(filenames=NULL, groups = NULL, groupnames = NULL, plot = > + TRUE, pca = TRUE, squarepca = FALSE, plottype="pdf", express = > c("rma"), addname = NULL, phenoData = new("phenoData")) > Background correcting > Normalizing > Calculating Expression > Error in hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > : > 'x' must be numeric > In addition: Warning message: > Incompatible phenoData object. Created a new one. > in: read.affybatch(filenames = filenames, phenoData = phenoData) > > Enter a frame number, or 0 to exit > > 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = > TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = > c("rma"), addname > 2: plotHist(dat, filenames) > 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > > Selection: > Enter an item from the menu, or 0 to exit > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "angle" "axes" "border" "breaks" > "col" "density" "freq" "include.lowest" > [9] "labels" "main" "nclass" "plot" > "probability" "right" "x" "xlab" > [17] "xlim" "ylab" "ylim" > Browse[1]> x > AffyBatch object > size of arrays=834x834 features (70650 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=13 > number of genes=31099 > annotation=rat2302 > Browse[1]> c > > Enter a frame number, or 0 to exit > > 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = > TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = > c("rma"), addname > 2: plotHist(dat, filenames) > 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > > Selection: 0 > >>sessionInfo() > > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" > "methods" "tools" "base" > > other attached packages: > rat2302cdf affyQCReport simpleaffy affycoretools biomaRt > RCurl XML GOstats Category genefilter > survival > "1.14.0" "1.12.0" "2.8.0" "1.6.0" "1.8.1" > "0.8-0" "1.2-0" "2.0.4" "2.0.3" "1.12.0" > "2.30" > KEGG RBGL annotate GO graph > RWinEdt limma affy affyio Biobase > "1.14.1" "1.10.0" "1.12.1" "1.14.1" "1.12.0" > "1.7-5" "2.9.1" "1.12.2" "1.2.0" "1.12.2" > > > Mark W. Kimpel MD > > > > > > Official Business Address: > > > > Department of Psychiatry > > Indiana University School of Medicine > > PR M116 > > Institute of Psychiatric Research > > 791 Union Drive > > Indianapolis, IN 46202 > > _______________________________________________ > 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 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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.

ADD COMMENT • link 18.0 years ago James W. MacDonald 67k

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Jim, Reinstalling Affy fixed the problem. Strange indeed. Thanks for your help this holiday weekend. Mark Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Saturday, December 23, 2006 4:35 PM To: Kimpel, Mark William Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with hist.default in affystart in package affycoretools Hi Mark, That is a weird error. It appears that hist.default() is being called on your AffyBatch object, rather than the hist() method defined in the affy package. Since you appear to have the affy package loaded, I have to assume for some reason it didn't load correctly because the method isn't getting found. If you restart R and try again, do you get the same result? You might also try just building an AffyBatch object and calling hist(abatch). If this continues, you might have a bum install of affy that may be repaired by re-installing. Best, Jim Kimpel, Mark William wrote: > I haven't used affycoretools since migrating to R 2.4.0 and BioC 1.9, > but code that used to work has stopped working. I have tried to use > affystart on two separate datasets and get the same error in > hist.default. It looks to me like an affy.object is being passed as an > argument to a function that does not accept it. In the code example > below I have used all of the affystart defaults, but I get the same > error if I supply arguments. > > Output, debugging info and sessionInfo are below. > > Thanks, > > Mark > > affystart(filenames=NULL, groups = NULL, groupnames = NULL, plot = > + TRUE, pca = TRUE, squarepca = FALSE, plottype="pdf", express = > c("rma"), addname = NULL, phenoData = new("phenoData")) > Background correcting > Normalizing > Calculating Expression > Error in hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > : > 'x' must be numeric > In addition: Warning message: > Incompatible phenoData object. Created a new one. > in: read.affybatch(filenames = filenames, phenoData = phenoData) > > Enter a frame number, or 0 to exit > > 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = > TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = > c("rma"), addname > 2: plotHist(dat, filenames) > 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > > Selection: > Enter an item from the menu, or 0 to exit > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "angle" "axes" "border" "breaks" > "col" "density" "freq" "include.lowest" > [9] "labels" "main" "nclass" "plot" > "probability" "right" "x" "xlab" > [17] "xlim" "ylab" "ylim" > Browse[1]> x > AffyBatch object > size of arrays=834x834 features (70650 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=13 > number of genes=31099 > annotation=rat2302 > Browse[1]> c > > Enter a frame number, or 0 to exit > > 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = > TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf", express = > c("rma"), addname > 2: plotHist(dat, filenames) > 3: hist(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > 4: hist.default(dat, lty = cl, lwd = 2, col = 1:length(filenames)) > > Selection: 0 > >>sessionInfo() > > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" > "methods" "tools" "base" > > other attached packages: > rat2302cdf affyQCReport simpleaffy affycoretools biomaRt > RCurl XML GOstats Category genefilter > survival > "1.14.0" "1.12.0" "2.8.0" "1.6.0" "1.8.1" > "0.8-0" "1.2-0" "2.0.4" "2.0.3" "1.12.0" > "2.30" > KEGG RBGL annotate GO graph > RWinEdt limma affy affyio Biobase > "1.14.1" "1.10.0" "1.12.1" "1.14.1" "1.12.0" > "1.7-5" "2.9.1" "1.12.2" "1.2.0" "1.12.2" > > > Mark W. Kimpel MD > > > > > > Official Business Address: > > > > Department of Psychiatry > > Indiana University School of Medicine > > PR M116 > > Institute of Psychiatric Research > > 791 Union Drive > > Indianapolis, IN 46202 > > _______________________________________________ > 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 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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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