[BioC] problem with hist.default in affystart in package affycoretools
Kimpel, Mark William
mkimpel at iupui.edu
Sat Dec 23 23:47:35 CET 2006
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 at 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
>
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--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
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