[BioC] arrayQualityMetrics and NChannelSets

[Wolfgang Huber]

Dear Tim

thank you for your feedback and sorry for the delayed reply. 
arrayQualityMetrics has changed a lot recently, and there may be some 
hickups.

Can you please try with a more recent (devel) version of 
arrayQualityMetrics, and if the problem persists, send me the offending 
object 'nc'?

As a quick workaround, can you try with converting to 'ExpressionSet' 
instead of 'NChannelSet'?

I have just tried

library(CCl4)
library(arrayQualityMetrics)
data(CCl4)
arrayQualityMetrics(CCl4)

which worked without error,and also this quality report
http://www-huber.embl.de/users/whuber/bioc-list/110916/Report_for_nCCl4_with_RIN 
was made by code in the package vignette from the NChannelSet nCCl4.

	Best wishes
	Wolfgang


 > sessionInfo()
R Under development (unstable) (2011-09-25 r57072)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] arrayQualityMetrics_3.9.4 CCl4_1.0.9
[3] limma_3.9.18              Biobase_2.13.9
[5] fortunes_1.4-2

loaded via a namespace (and not attached):
  [1] AnnotationDbi_1.15.21 BiocInstaller_1.1.28  Biostrings_2.21.9
  [4] Cairo_1.4-9           DBI_0.2-5             Hmisc_3.8-3
  [7] IRanges_1.11.27       KernSmooth_2.23-6     RColorBrewer_1.0-5
[10] RSQLite_0.9-4         SVGAnnotation_0.9-0   XML_3.4-3
[13] affy_1.31.5           affyPLM_1.29.3        affyio_1.21.2
[16] annotate_1.31.1       beadarray_2.3.8       cluster_1.14.0
[19] genefilter_1.35.0     grid_2.14.0           hwriter_1.3
[22] lattice_0.19-33       latticeExtra_0.6-18   preprocessCore_1.15.0
[25] reshape_0.8.4         setRNG_2009.11-1      splines_2.14.0
[28] survival_2.36-9       tools_2.14.0          vsn_3.21.2
[31] xtable_1.5-6          zlibbioc_0.1.7



Sep/22/11 12:29 PM, Tim Rayner scripsit::
> Hi,
>
> Just a quick note to observe that the current stable version of
> arrayQualityMetrics seems to have a problem with NChannelSet objects:
>
>> nc
> NChannelSet (storageMode: lockedEnvironment)
> assayData: 1178100 features, 50 samples
>    element names: exprs
> protocolData
>    rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ...
>      GWAS16.L_148_CD16.CEL (50 total)
>    varLabels: exprs dates
>    varMetadata: labelDescription channel
> phenoData
>    rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ...
>      GWAS16.L_148_CD16.CEL (50 total)
>    varLabels: info.batch.name operator ... visual_check (62 total)
>    varMetadata: labelDescription channel
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: pd.hugene.1.1.st.v1
>
>
>> arrayQualityMetrics(nc)
> The directory 'arrayQualityMetrics report for nc' has been created.
> Error in rep("#1F78B4", x$numArrays) : invalid 'times' argument
>
>
>> traceback()
> 4: intgroupColors(x)
> 3: append(x, intgroupColors(x))
> 2: prepdata(expressionset, intgroup = intgroup, do.logtransform =
> do.logtransform)
> 1: arrayQualityMetrics(nc)
>
>
>> validObject(nc)
> [1] TRUE
>
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] arrayQualityMetrics_3.8.0 pd.hugene.1.1.st.v1_3.2.0
>   [3] oligo_1.16.0              preprocessCore_1.14.0
>   [5] oligoClasses_1.14.0       RSQLite_0.9-4
>   [7] DBI_0.2-5                 ClinStudyWeb_0.2.4
>   [9] rjson_0.2.5               SmithLabArray_0.5.5
> [11] limma_3.8.3               Biobase_2.12.2
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.24.0    affy_1.30.0          affyio_1.20.0
>   [4] affyPLM_1.28.5       annotate_1.30.1      AnnotationDbi_1.14.1
>   [7] beadarray_2.2.0      Biostrings_2.20.3    bit_1.1-7
> [10] Cairo_1.4-9          cluster_1.14.0       ff_2.2-3
> [13] gdata_2.8.1          genefilter_1.34.0    gplots_2.10.1
> [16] grid_2.13.1          gtools_2.6.2         Hmisc_3.8-3
> [19] hopach_2.12.0        hwriter_1.3          IRanges_1.10.6
> [22] lattice_0.19-33      latticeExtra_0.6-18  RColorBrewer_1.0-5
> [25] RCurl_1.6-10         setRNG_2009.11-1     splines_2.13.1
> [28] survival_2.36-9      SVGAnnotation_0.9-0  tcltk_2.13.1
> [31] tools_2.13.1         vsn_3.20.0           XML_3.4-3
> [34] xtable_1.5-6
>
> Given that the documentation claims to support such objects I'm
> assuming this is a bug? I'm currently coercing GeneFeatureSet objects
> to NChannelSet and as you can see the conversion yields valid objects.
> As a workaround, is there an alternative class to which I should be
> coercing?
>
> Many thanks,
>
> Tim Rayner
>


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber