Unfortunately, you may want to be careful about making it too robust (depending on what you mean). For example filtering methods could very well be seen as replacing one matrix with a smaller one. Not sure if these methods use exprs<-, but that is probably how I would do it.
What would be better is if in the process of doing the replacement, the other slots are harmonized in a relevant way. That would require row names on the replacement matrix. Kasper On Fri, Jan 10, 2014 at 9:52 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > On 01/10/2014 12:07 AM, Maintainer wrote: > >> dear maintainers of Biobase and lumi, >> >> this is a question raised from a different thread a few days ago here: >> >> https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005129.html >> >> the matrix of genes by samples expression values in an 'ExpressionSet' >> object can be accessed and replaced with the "exprs<-" method and this >> changes automatically the dimension of the 'ExpressionSet' object as >> illustrated in the following example: >> >> library(Biobase) >> >> data(sample.ExpressionSet) >> dim(sample.ExpressionSet) >> Features Samples >> 500 26 >> exprs(sample.ExpressionSet) <- matrix(rnorm(2600), nrow=100) >> dim(sample.ExpressionSet) >> Features Samples >> 100 26 >> >> however, this does not seem to be happening with 'LumiBatch' objects >> which are an extension of 'ExpressionSet' objects: >> >> library(lumi) >> >> data(example.lumi) >> dim(example.lumi) >> Features Samples >> 8000 4 >> exprs(example.lumi) <- matrix(rnorm(400), nrow=100) >> dim(example.lumi) ## NOTE NOW THAT DIMENSION DOES NOT CHANGE!! >> Features Samples >> 8000 4 >> > > actually, the expression values have been replaced > > > dim(exprs(example.lumi)) > [1] 100 4 > > but the object is no longer valid > > > validObject(example.lumi) > Error in validObject(example.lumi) : > invalid class "LumiBatch" object: row numbers differ for assayData > members > > This is also true of the ExpressionSet example (the object is no longer > valid), it's just that the dims are taken from a different location so > reflect the addition. > > The user should be providing expression values with the same dimensions > (and with the same dimnames) as the original. I think the intended use case > was more along the lines of replacing the expression matrix with say a > transformed version, exprs(x) = log(exprs(x)). > > Obviously Biobase shouldn't be allowing the user to see an invalid object, > but the design of the package does not make it easy to enforce this; I'll > work on providing something more robust, but the end result of trying the > above assignment will be an error. > > Martin > > > >> a couple of diagnostics are that the expression matrix itself it does >> seem to have been replaced: >> >> dim(exprs(example.lumi)) >> [1] 100 4 >> >> and the "exprs<-" method does not seem to be explicitely defined for >> 'LumiBatch' objects: >> >> showMethods("exprs") >> Function: exprs (package Biobase) >> object="AffyBatch" >> object="ExpressionSet" >> object="MethyLumiSet" >> object="SnpSet" >> >> so i guess something is not working at the interaction of >> Biobase::exprs<- and LumiBatch-class, whether this should be fixed at >> Biobase or lumi, have no idea. >> >> thanks! >> robert. >> ps: sessionInfo() >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C >> LC_TIME=en_US.UTF8 >> [4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8 >> LC_MESSAGES=en_US.UTF8 >> [7] LC_PAPER=en_US.UTF8 LC_NAME=C LC_ADDRESS=C >> >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] lumi_2.14.1 Biobase_2.22.0 BiocGenerics_0.8.0 >> vimcom_0.9-92 >> [5] setwidth_1.0-3 colorout_1.0-1 >> >> loaded via a namespace (and not attached): >> [1] affy_1.40.0 affyio_1.30.0 annotate_1.40.0 >> [4] AnnotationDbi_1.24.0 base64_1.1 beanplot_1.1 >> [7] BiocInstaller_1.12.0 biomaRt_2.18.0 Biostrings_2.30.1 >> [10] bitops_1.0-6 BSgenome_1.30.0 bumphunter_1.2.0 >> [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> [16] digest_0.6.4 doRNG_1.5.5 foreach_1.4.1 >> [19] genefilter_1.44.0 GenomicFeatures_1.14.2 GenomicRanges_1.14.4 >> [22] grid_3.0.2 illuminaio_0.4.0 IRanges_1.20.6 >> [25] iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 >> [28] lattice_0.20-24 limma_3.18.7 locfit_1.5-9.1 >> [31] MASS_7.3-29 Matrix_1.1-1.1 matrixStats_0.8.14 >> [34] mclust_4.2 methylumi_2.8.0 mgcv_1.7-27 >> [37] minfi_1.8.9 multtest_2.18.0 nleqslv_2.1 >> [40] nlme_3.1-113 nor1mix_1.1-4 pkgmaker_0.17.4 >> [43] preprocessCore_1.24.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [46] registry_0.2 reshape_0.8.4 R.methodsS3_1.6.1 >> [49] rngtools_1.2.3 Rsamtools_1.14.2 RSQLite_0.11.4 >> [52] rtracklayer_1.22.0 siggenes_1.36.0 splines_3.0.2 >> [55] stats4_3.0.2 stringr_0.6.2 survival_2.37-4 >> [58] tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 >> [61] XVector_0.2.0 zlibbioc_1.8.0 >> >> ________________________________________________________________________ >> devteam-bioc mailing list >> To unsubscribe from this mailing list send a blank email to >> devteam-bioc-le...@lists.fhcrc.org >> You can also unsubscribe or change your personal options at >> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
