[BioC] Error in QAReport function of package affyQCReport

[Mark W Kimpel]

Robert,

You are correct, I am using the function QCReport. I downloaded the 
source code of the packages affy and affyQCReport and believe the 
problem may be that the wrong method is being called when boxplot is 
invoked on my affybatch object. I get an error when I do 
signature(affy.batch). See below... Is this expected behavior? Could my 
affybatch object be corrupted?  Mark

 > signature(affy.batch)
Error in signature(affy.batch) :
   bad class specified for element 1 (should be a single character string)

Enter a frame number, or 0 to exit

1: signature(affy.batch)

Selection: 1
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
[1] "i"     "names" "sigi"  "value"
Browse[1]> value
[[1]]
AffyBatch object
size of arrays=834x834 features (23 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=80
number of genes=31099
annotation=rat2302
notes=

Browse[1]> i
[1] 1
Browse[1]> names
NULL
Browse[1]> sigi
AffyBatch object
size of arrays=834x834 features (23 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=80
number of genes=31099
annotation=rat2302
notes=
Browse[1]>

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
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Robert Gentleman wrote:
> It looks to me like you are using a function named QCReport, not 
> QAReport (and indeed there is no such thing - you might look at 
> affyQAReport, which is in the same package but is very different).
> 
> You can try to see what is happening by looking at the code from 
> signalDist:
> 
> par(mfrow=c(2, 1))
> ArrayIndex = as.character(1:length(sampleNames(object)))
> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index")
> 
> 
> where instead of object you use affy.batch.sub. The code looks pretty 
> straightforward, so I don't know what the problem might be.  It is a bit 
> odd, it seems to me to use integers in place of the sample names...
> 
> I used the affybatch.example and it worked for me.. ( one issue with 
> that was
> Warning message:
> In data.row.names(row.names, rowsi, i) :
>   some row.names duplicated: 
> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, 
> 
> ....
> 
> which we may need to look at).
> 
> best wishes
>   Robert
> 
> 
> Mark W Kimpel wrote:
>> I am running into an error when I run QAReport on an affybatch object. 
>> Below is my sessionInfo and output. I am using the devel versions of R 
>> and BioC, all newly updated. Please advise.
>>
>> Thanks,
>> Mark
>>
>> Browse[1]> sessionInfo()
>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095)
>> i686-pc-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] grDevices datasets  splines   graphics  stats     tools     utils
>> [8] methods   base
>>
>> other attached packages:
>>   [1] hgu95av2cdf_1.17.0     rat2302cdf_1.17.0      affyQCReport_1.15.2
>>   [4] geneplotter_1.15.2     lattice_0.16-2         RColorBrewer_1.0-1
>>   [7] affyPLM_1.13.6         affydata_1.11.2        simpleaffy_2.11.21
>> [10] affycoretools_1.9.2    annaffy_1.9.1          xtable_1.4-6
>> [13] gcrma_2.9.1            matchprobes_1.9.10     biomaRt_1.11.4
>> [16] RCurl_0.8-1            XML_1.9-0              GOstats_2.3.8
>> [19] Category_2.3.16        genefilter_1.15.3      survival_2.32
>> [22] KEGG_1.17.0            RBGL_1.13.3            annotate_1.15.2
>> [25] AnnotationDbi_0.0.83   RSQLite_0.6-0          DBI_0.2-3
>> [28] GO_1.17.0              graph_1.15.10          limma_2.11.9
>> [31] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.6
>> [34] Biobase_1.15.21
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.7     grid_2.6.0         KernSmooth_2.22-20
>>
>>  > affy.batch.sub
>> AffyBatch object
>> size of arrays=834x834 features (14 kb)
>> cdf=Rat230_2 (31099 affyids)
>> number of samples=16
>> number of genes=31099
>> annotation=rat2302
>> notes=
>>  > QCReport(affy.batch.sub)
>> Error in attr(groups, "names") <- names :
>>    'names' attribute [16] must be the same length as the vector [1]
>>
>> Enter a frame number, or 0 to exit
>>
>> 1: QCReport(affy.batch.sub)
>> 2: signalDist(object)
>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab 
>> = "Array
>> 4: boxplot.default(object, names = ArrayIndex, ylab = 
>> "Log2(Intensity)", xlab
>>
>> Selection: 4
>> Called from: eval(expr, envir, enclos)
>> Browse[1]> ls()
>>   [1] "add"        "args"       "at"         "border"     "col"
>>   [6] "groups"     "horizontal" "log"        "n"          "namedargs"
>> [11] "names"      "notch"      "outline"    "pars"       "plot"
>> [16] "range"      "*tmp*"      "varwidth"   "width"      "x"
>> Browse[1]> names
>>   [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13" 
>> "14" "15"
>> [16] "16"
>> Browse[1]> names(group)
>> NULL
>> Browse[1]> names(groups)
>> [1] ""
>> Browse[1]> names(groups) <- names
>> Error during wrapup: 'names' attribute [16] must be the same length as 
>> the vector [1]
>> Browse[1]>
>