[Bioc-devel] [devteam-bioc] problem w/ "exprs<-" method and LumiBatch objects

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 <mtmorgan at fhcrc.org
<mailto:mtmorgan at 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
        <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    but the object is no longer valid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    This is also true of the ExpressionSet example (the object is no
    longer valid), it's just that the dims are taken from a different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