[BioC] affyQCReport with drosgenome2cdf

[James W. MacDonald]

Hi Assa,

You might try the arrayQualityMetrics package.

Best,

Jim



On 11/15/2010 4:59 AM, Assa Yeroslaviz wrote:
> Hi everybody,
>
> I have a set of drosophile genome 2.0 arrays to analyze. I wanted to
> start with a quality control using the affyQCReport package.
>
> according to the manual I set the enivironment.
>> setQCEnvironment("drosgenome2cdf", "/home/AYeroslaviz/R/x86_64-pc-linux-gnu-library/2.12/simpleaffy/extdata")
>
> and run the QCreport on the raw data
>> QCReport(rawData)
>
> unfortunately I get an error message
>
> Error: NAs in foreign function call (arg 5)
>
> Can someone please tell me what the meaning of this error. I tried to
> search the mailing lists but didn't find anything.
> If AffyQCReport doesn't work, do I have an alternative?
>
> Thanks
>
> Assa
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
>   [1] tools     tcltk     splines   stats     graphics  grDevices utils
>   [8] datasets  methods   base
>
> other attached packages:
>   [1] simpleaffy_2.26.0         genefilter_1.32.0
>   [3] drosophila2cdf_2.7.0      arrayQualityMetrics_3.2.1
>   [5] vsn_3.18.0                affyPLM_1.26.0
>   [7] gcrma_2.22.0              tkWidgets_1.28.0
>   [9] widgetTools_1.28.0        siggenes_1.24.0
> [11] multtest_2.6.0            samr_1.28
> [13] impute_1.24.0             MASS_7.3-5
> [15] vioplot_0.2               sm_2.2-4.1
> [17] preprocessCore_1.10.0     DynDoc_1.28.0
> [19] cluster_1.13.1            affydata_1.11.10
> [21] affycomp_1.26.0           affyQCReport_1.28.0
> [23] lattice_0.19-13           affy_1.28.0
> [25] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.16.0        annotate_1.28.0      AnnotationDbi_1.12.0
>   [4] beadarray_2.0.2      Biostrings_2.18.0    DBI_0.2-5
>   [7] grid_2.12.0          hwriter_1.2          IRanges_1.8.2
> [10] latticeExtra_0.6-14  limma_3.6.6          marray_1.28.0
> [13] RColorBrewer_1.0-2   RSQLite_0.9-1        stats4_2.12.0
> [16] survival_2.35-8      SVGAnnotation_0.7-2  XML_2.6-0
> [19] xtable_1.5-6
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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