Entering edit mode
Mark W Kimpel
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830
@mark-w-kimpel-2027
Last seen 10.3 years ago
I am getting an error with QCReport of package affyQCReport. Debugging
info and sessionInfo() follows. It looks to me like the group
attributes
is not being extracted properly from the affyObject. SampleNames that
match the CEL files are stored in the first column of Data.
I am using the current version of R and BioC packages, not the devel
versions.
Thanks,
Mark
> ?QCReport
> paste(experiment.designator, "AffyQCReport.pdf", sep=".")
[1] "RL02.AffyQCReport.pdf"
> QCReport(object=affy.object,file=paste(experiment.designator,
"AffyQCReport.pdf", sep="."))
Error in attr(groups, "names") <- names : 'names' attribute [29] must
be
the same length as the vector [1]
Enter a frame number, or 0 to exit
1: QCReport(object = affy.object, file = paste(experiment.designator,
"AffyQCReport.pdf", sep = "."))
2: signalDist(object)
3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab =
"Array Index")
4: boxplot.default(object, names = ArrayIndex, ylab =
"Log2(Intesity)",
xlab = "Array Index")
Selection: 2
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
[1] "ArrayIndex" "object"
Browse[1]> ArrayIndex
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13"
"14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27"
"28" "29"
Browse[1]> object
AffyBatch object
size of arrays=834x834 features (157603 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=29
number of genes=31099
annotation=rat2302
Browse[1]> c
Enter a frame number, or 0 to exit
1: QCReport(object = affy.object, file = paste(experiment.designator,
"AffyQCReport.pdf", sep = "."))
2: signalDist(object)
3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab =
"Array Index")
4: boxplot.default(object, names = ArrayIndex, ylab =
"Log2(Intesity)",
xlab = "Array Index")
Selection: 3
Called from: eval(expr, envir, enclos)
Browse[1]> boxplot
function (x, ...)
UseMethod("boxplot")
<environment: namespace:graphics="">
Browse[1]> ls()
[1] "x"
Browse[1]> x
AffyBatch object
size of arrays=834x834 features (157603 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=29
number of genes=31099
annotation=rat2302
Browse[1]> c
Enter a frame number, or 0 to exit
1: QCReport(object = affy.object, file = paste(experiment.designator,
"AffyQCReport.pdf", sep = "."))
2: signalDist(object)
3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab =
"Array Index")
4: boxplot.default(object, names = ArrayIndex, ylab =
"Log2(Intesity)",
xlab = "Array Index")
Selection: 4
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
[1] "*tmp*" "add" "args" "at" "border"
"col" "groups" "horizontal" "log" "n"
"namedargs"
[12] "names" "notch" "outline" "pars" "plot"
"range" "varwidth" "width" "x"
Browse[1]> dim(x)
NULL
Browse[1]> names
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13"
"14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27"
"28" "29"
Browse[1]> attr(groups,names)
Error during wrapup: exactly one attribute 'name' must be given
Browse[1]> groups
[[1]]
AffyBatch object
size of arrays=834x834 features (157603 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=29
number of genes=31099
annotation=rat2302
Browse[1]> c
Enter a frame number, or 0 to exit
1: QCReport(object = affy.object, file = paste(experiment.designator,
"AffyQCReport.pdf", sep = "."))
2: signalDist(object)
3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab =
"Array Index")
4: boxplot.default(object, names = ArrayIndex, ylab =
"Log2(Intesity)",
xlab = "Array Index")
Selection: 0
> sessionInfo()
R version 2.4.1 (2006-12-18)
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" "tools" "methods" "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
Neuroinformatics
Department of Psychiatry
Indiana University School of Medicine