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

[Martin Morgan]

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but the object is no longer valid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This is also true of the ExpressionSet example (the object is no longer valid), 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
>
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