[BioC] arrayQualityMetrics Error

[Groot, Philip de]

Hello all,
 
Please note that MAS5 won't work for PM-only arrays! So creating your own .qcdef file is pretty useless here...
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Mon 11-1-2010 14:52
To: Ramzi TEMANNI
Cc: Bioconductor Newsgroup
Subject: Re: [BioC] arrayQualityMetrics Error



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
>
>       [[alternative HTML version deleted]]
>
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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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