[BioC] Error in QAReport function of package affyQCReport
Robert Gentleman
rgentlem at fhcrc.org
Sun Jul 29 00:44:13 CEST 2007
Mark W Kimpel wrote:
> 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
It could well be, but that is not what signature is for.
You want class(affy.batch) - but you were using a subset of that I
thought. It is possible to get both corrupted objects (especially if
they are old and may have been created with a previous version of R) and
also method dispatch can get confused.
I cannot tell from what you have sent which is like to be your problem.
Please check the class of the object, and also run the code I sent in
the previous email with all output, that might help to figure out just
what your problem is. It might also help to see the output of search
and potentially of showMethods.
I get:
> showMethods("boxplot")
Function: boxplot (package graphics)
x="ANY"
x="AffyBatch"
with the affy package attached.
best wishes
Robert
>
> > 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
> (317) 663-0513 Home (no voice mail please)
>
> ******************************************************************
>
> 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]>
>>
>
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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