[BioC] Error in QAReport function of package affyQCReport

[Robert Gentleman]

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