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.



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"





> 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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