[BioC] error with AffyQCReport

[Wolfgang Huber]

Dear Mark,

the parts of Biobase and of the affyQCReport packages that may be
involved in your problem have changed quite a lot since the 1.9 release.
Would you mind trying to see whether you get the same (or another)
problem with a current R-devel and the devel versions of the packages?
Otherwise we may end up chasing bugs that are long gone...

 Best wishes
 Wolfgang



 W Kimpel wrote:
> 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"
> 


-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber