[BioC] AnnotatedDataFrame metadata bug?

[Martin Morgan]

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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
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