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

[Kimpel, Mark William]

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 

 

 

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Department of Psychiatry

Indiana University School of Medicine

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