[BioC] arrayQualityMetrics Error

[James W. MacDonald]

Hi Ramzi,

Ramzi TEMANNI wrote:
> Hi,
> I'm runing some QC analysis with 5 Affy mouse genechip HT430PM
> I've installed the required libraries(affy, arrayQualityMetrics,
> htmg430pmcdf) and all dependecies
> I'm using the following code:
> fls <- list.files("/", ".*CEL")
> eset <- justRMA(filenames = fls)
> aBatch <- ReadAffy(filenames = fls)
> arrayQualityMetrics(aBatch,outdir = "report")
> 
> The last commad shows the following error message:
> 
> The report will be written in directory 'report'.
> Error in setQCEnvironment(cdfn) :
>   Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy
> does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters
> manually.

This seems pretty clear to me. The simpleaffy package does not have the 
QC parameters for this array and there is some explanation of how to fix 
this in the package vignette. Did you look in the package vignette to 
see how to fix it?

Note that the htmg430pm chip is quite similar to the moe430 chip, so the 
QC parameters will likely be the same, but you might need to adjust the 
names of the QC probes.

Best,

Jim

> 
> Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
>   'x' contains missing values
> In addition: Warning message:
> In aqm.qcstats(expressionset) :
>   'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
> In addition: Warning message:
> In arrayQualityMetrics(aBatch, outdir = "report") :
>   Cannot draw the Perfect Match versus MisMatch plot
> 
> Any idea about the orgin of this error ?
> Thanks in advance for your help.
> Kind regards
> Ramzi
> ----------------------------------------------------------------
> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
> 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] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0
> [3] preprocessCore_1.8.0      gcrma_2.18.0
> [5] htmg430pmcdf_2.5.0        affy_1.24.2
> [7] Biobase_2.6.1
> loaded via a namespace (and not attached):
>  [1] affyio_1.14.0       annotate_1.24.0     AnnotationDbi_1.8.1
>  [4] beadarray_1.14.0    Biostrings_2.14.8   DBI_0.2-4
>  [7] genefilter_1.28.2   grid_2.10.1         hwriter_1.1
> [10] IRanges_1.4.9       lattice_0.17-26     latticeExtra_0.6-4
> [13] limma_3.2.1         marray_1.24.0       RColorBrewer_1.0-2
> [16] RSQLite_0.7-3       simpleaffy_2.22.0   splines_2.10.1
> [19] stats4_2.10.1       survival_2.35-8     tcltk_2.10.1
> [22] tools_2.10.1        vsn_3.14.0          xtable_1.5-6
> 
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> 
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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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