[BioC] problem with hist.default in affystart in package affycoretools

[James W. MacDonald]

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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