[BioC] error with AffyQCReport

[Mark W Kimpel]

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