[BioC] AnnotatedDataFrame metadata bug?
Martin Morgan
mtmorgan at fhcrc.org
Thu Feb 20 02:45:25 CET 2014
On 02/19/2014 03:03 PM, Adrienne Stilp wrote:
> Hi Bioconductors,
>
> I recently noticed some unexpected behavior for AnnotatedDataFrame metadata. If you have an annotated data frame with metadata and add a new variable whose name is a shortened version of an existing variable, the metadata for the newly-added variable is set to the metadata of the existing variable. Here's an example:
>
> library(Biobase)
>
> annot <- AnnotatedDataFrame(data.frame(myvariable=runif(10)))
> varMetadata(annot)["myvariable", "labelDescription"] <- "random samples from a uniform distribution"
>
> annot$myvar <- rnorm(10)
> annot$newvar <- rnorm(10)
> annot[["myvari"]] <- rnorm(10)
>
> varMetadata(annot)
>
>
> For me, this last step prints out:
>
> labelDescription
> myvariable random samples from a uniform distribution
> myvar random samples from a uniform distribution
> newvar <NA>
> myvari random samples from a uniform distribution
>
Thanks for the bug report; this is fixed in Biobase 2.23.5, which will appear in
the devel branch probably on Friday. Martin
>
> even though I've only set the metadata for myvariable. I would expect that any new variables have NA for metadata, which is true for "newvar" above, but is not the case for the variables whose names are a shortened version of "myvariable" ("myvar" and "myvari"). I end up with misleading or incorrect metadata for the new variables "myvar" and "myvari". The can always be changed later, but I often see what metadata I need to update at the end by checking which have NA labelDescriptions, so these new variables wouldn't show up.
>
>
> I'm using bioc-devel. Here's the sessionInfo() output:
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] Biobase_2.22.0 BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
>
> Thanks,
> Adrienne
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