[BioC] Error in QAReport function of package affyQCReport
Mark W Kimpel
mwkimpel at gmail.com
Sun Jul 29 04:20:13 CEST 2007
Seth and Robert,
Looks like I may have more than one problem. To clarify one point first,
in my original post I was using affy.batch.sub, which consisted of just
some of the arrays from my affy.batch. To make sure I'm not having a
problem with subsetting, in my subsequent posts I am using the affybatch
object created just today with ReadAffy. No old versions here, just what
comes out of my sessionInfo().
As you can see below, there may be a problem with my boxplot method but
also with the affybatch object. The latter is of class AffyBatch but is
not a valid object.
Thanks, Mark
> class(affy.batch)
[1] "AffyBatch"
attr(,"package")
[1] "affy"
> require(affy)
> showMethods("boxplot")
Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) :
variable ".AllMTable" was not found
Enter a frame number, or 0 to exit
1: showMethods("boxplot")
2: .showMethodsTable(getGeneric(f, where = where), includeDefs,
inherited, cla
3: get(if (inherited) ".AllMTable" else ".MTable", envir = env)
> validObject(affy.batch)
Error in validObject(affy.batch) :
invalid class "AffyBatch" object: sampleNames differ between
assayData and phenoData
Enter a frame number, or 0 to exit
1: validObject(affy.batch)
> par(mfrow=c(2, 1))
> ArrayIndex = as.character(1:length(sampleNames(affy.batch)))
>
boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array
Index")
Error in attr(groups, "names") <- names :
'names' attribute [80] must be the same length as the vector [1]
Enter a frame number, or 0 to exit
1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)",
xlab = "A
2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)",
xlab = "A
3: boxplot.default(affy.batch, names = ArrayIndex, ylab =
"Log2(Intensity)", x
Selection:
---
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]>
>
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