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 asRG.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 [[alternative HTML version deleted]]

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 asRG.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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor