Entering edit mode
@denrique-escobar-espinoza-1303
Last seen 11.2 years ago
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
>>>>>>>>>>>>>>>>>>>>>>>
