[BioC] Error in function (classes, fdef, mtable)

D.Enrique ESCOBAR ESPINOZA escobarebio at yahoo.com
Fri Nov 24 18:19:21 CET 2006


I would like some help to solve my little problem using affyQCReport:
I don t know why but I m having troubles to call proper libraries.
I wrote the following method:
=============================
#* @param		aPrefix	a string representing a png filename
#* @param		aData	an AffyBatch object to plot
plotCorr2png	<- function	(aTitle	= "",
							aData	= NULL
							){
				doCat	(":::::::plotCorr2png::")
				print(aTitle)
				print(aData)
				require(affyQCReport)
				print(sessionInfo())
				aTitlePNG	= paste(aTitle,"Corr.png",sep="")
				png	(filename=aTitlePNG,
					width=600,height=800,res=600)
					
					correlationPlot(aData)
					
				dev.off()
				pkg		<- "package:affyQCReport";
				detach(pos = match(pkg, search()))
}
==============================
the error appear when I plot into apng file
correlationPlot...
It use to say no correlationPlot function, i solved that requiring
affyQCReport.
Then I m still having the output even if simpleaffy is loaded
>>>>>>>>>>>>>>>>>>>>>>>
:::::::plotCorr2png::
[1] "affylimsgenechipanalyze-doVESICULES-qc_AffyQC"
AffyBatch object
size of arrays=1002x1002 features (39230 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=5
number of genes=45101
annotation=mouse4302
Loading required package: affyQCReport
Welcome to 'affyQCReport' V 1.6-1
Further information available at: www.bifix.org
      mailto: craig.parman at bifix.org
R version 2.4.0 (2006-10-03)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics" 
"grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
affyQCReport   simpleaffy   reposTools   genefilter     survival     
 xtable
    "1.10.0"      "2.6.0"     "1.10.0"     "1.12.0"       "2.29"     
"1.4-2"
mouse4302cdf      affyPLM        gcrma  matchprobes     affydata     
   affy
    "1.12.0"     "1.10.0"      "2.6.0"      "1.6.0"     "1.10.0"    
"1.12.1"
      affyio      Biobase
     "1.0.0"     "1.12.2"
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "pData", for
signature "phenoData"
In addition: Warning message:
X11 used font size 25 when 28 was requested
Execution halted
Total files in  directory  : 47
>>>>>>>>>>>>>>>>>>>>>>>



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