[BioC] arrayQualityMetrics

[Martin Morgan]

santana sarma wrote:
> Hi All,
> 
> Any help on the following would be appreciated:
> 
> 1. For Affymetrix data, function(s) like MAplot produces a summary
> statistics along with a trendline of the data. Wonder if there is a function
> that outputs somewhat similarly for cDNA data too !
> 
> 2. To the output of Limma's normalization (*normalizeWithinArrays* and then,
> *normalizeBetweenArrays*), as I try to use arrayQualityMetrics, an error
> message comes up.
> 
> arrayQualityMetrics (BetArray_Scale, force=TRUE)   # BetArray_Scale is an
> "MAList" from betweenArrayNormalization
> 
> 
> 
> Error in validObject(.Object) :
> 
>   invalid class "ExpressionSet" object: sampleNames differ between assayData
> and phenoData
> 
> Error in arrayQualityMetrics(BetArray_Scale, force = TRUE) :
> 
>   The expressionset is a MAList and cannot be converted automatically in a
> ExpressionSet. Try to convert it manually.

Hi Santana --

This is likely occurring because colnames(BetArray_Scale$M) do not equal
rownames(BetArray_Scale$targets). This might be because you've assembled
the MAList yourself, rather than using limma appropriately. You should
track down when in your work flow the colnames of M differ from the
rownames of targets, likely you've associated the wrong phenotypic and
array data. A little more below...

> 
> 
> 
> Then, while trying to convert it, again there is an error message.
> 
> x <- new ("MAList")
> 
> x$M <- BetArray_Scale$M
> 
> x$A <- BetArray_Scale$A
> 
> x$targets <- BetArray_Scale$targets
> 
> z <- as (RG.MA(x), "ExpressionSet")
> 
> Error in as(RG.MA(x), "ExpressionSet") :
> 
>   no method or default for coercing "RGList" to "ExpressionSet"


ExpressionSet is relatively down-stream in the analysis pipeline, after
normalization and summarization; it is approximately comparable to
MAList, but not RGList; for this reason there is no conversion from
RGList to ExpressionSet. Likely you want as(x, "ExpressionSet").

Martin

> 
> 
> 
> 
> 
>> sessionInfo ()
> 
> R version 2.9.0 (2009-04-17)
> 
> i386-pc-mingw32
> 
> 
> 
> locale:
> 
> 
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> 
> other attached packages:
> 
>  [1] geneplotter_1.22.0        lattice_0.17-22
> annotate_1.22.0
> AnnotationDbi_1.6.1       arrayQualityMetrics_2.2.2 affyPLM_1.20.0
> 
> 
>  [7] preprocessCore_1.6.0      gcrma_2.16.0
> Biostrings_2.12.7
> IRanges_1.2.3             affy_1.22.0               convert_1.20.0
> 
> 
> [13] marray_1.22.0             limma_2.18.2              Biobase_2.4.1
> 
> 
> 
> 
> loaded via a namespace (and not attached):
> 
>  [1] affyio_1.12.0      beadarray_1.12.0   DBI_0.2-4
> genefilter_1.24.2  grid_2.9.0         hwriter_1.1        latticeExtra_0.6-1
> RColorBrewer_1.0-2 RSQLite_0.7-1
> 
> [10] simpleaffy_2.20.0  splines_2.9.0      stats4_2.9.0
> survival_2.35-4    tools_2.9.0        vsn_3.12.0         xtable_1.5-5
> 
> 
> 
> Thank you.
> 
> 
> 
> Cheers,
> 
> Santana
> 
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> 
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