[BioC] [Bioc-devel] error with AffyQCReport

James W. MacDonald jmacdon at med.umich.edu
Tue Feb 6 23:10:20 CET 2007


Hi Mark,

Mark W Kimpel wrote:
> Wolfgang,
> 
> I installed a fresh build of R 2.5.0-devel 2 days ago and updated all my 
> devel packages today. I get the same error. See my debugging output 
> below. Note that read.AnnotatedDataFrame.ordered is my own function to 
> keep me from accidentally not ordering my text file in the same order as 
> my cel.files. The last I knew read.phenoData did not include this 
> feature and I really screwed up an analysis because of it. Anyway, my 
> function code it immediately below. I'm copying to BioC-devel list as 
> that might be the best place to continue this.
> 
> Thanks,
> Mark
> 
> #reads in unsorted phenodata type file and makes and adf. "adf.txt" MUST 
> have celfiles names without ".CEL" as sample names in first column
> ########################################################################
> read.AnnotatedDataFrame.ordered.func<-function(adf.file="adf.txt")
> {
> require(affy, quiet=TRUE)
> adf<-read.AnnotatedDataFrame(adf.file, header=TRUE, sep="\t", row.names=1)
> cel.files<-list.celfiles()
> pos<-pmatch(rownames(pData(adf)), cel.files)
> adf<-adf[pos,]
> adf
> }
> ############################################################
> #Session output
>  > #QC
>  > adf<-read.AnnotatedDataFrame.ordered.func()
>  >
>  > affy.object<-ReadAffy(phenoData=adf)
>  >
>  > 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]

What exactly is 'experiment.designator'? I can get this function to work 
(although I get a different warning I am trying to track down). What do 
you get when you do

paste(experiment.designator, "AffyQCReport.pdf", sep=".")

at an R prompt? From the error I am betting you get something of length 29.

Best,

Jim


> 
> 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]> 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]> groups
> [[1]]
> AffyBatch object
> size of arrays=834x834 features (182056 kb)
> cdf=Rat230_2 (31099 affyids)
> number of samples=29
> number of genes=695556
> annotation=rat2302
> notes=
> 
> 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 2.5.0 Under development (unstable) (2007-01-31 r40628)
> 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 lattice geneplotter RColorBrewer affyPLM gcrma 
> matchprobes affydata xtable simpleaffy
> "1.15.0" "1.13.16" "0.14-16" "1.12.0" "0.2-3" "1.11.13" "2.7.1" "1.7.4" 
> "1.11.1" "1.4-3" "2.9.1"
> affycoretools biomaRt RCurl XML GOstats Category genefilter survival 
> KEGG RBGL annotate
> "1.6.0" "1.6.3" "0.8-0" "1.4-1" "2.1.11" "2.1.11" "1.13.8" "2.31" 
> "1.15.1" "1.11.4" "1.13.6"
> GO graph limma affy affyio Biobase
> "1.15.1" "1.13.5" "2.9.9" "1.13.14" "1.3.3" "1.13.34"
> 
> Wolfgang Huber wrote:
> 
>>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"
>>>
>>>    
>>
>>
>>  
> 
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.



More information about the Bioconductor mailing list