Entering edit mode
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
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
