[Bioc-devel] initialize method for ExpressionSet

[Martin Morgan]

Hi Matthias --

Matthias Kohl wrote:
> Dear all,
> 
> just had a look at the initialize method for class ExpressionSet.
> 
> As far as I understand, the part "else if (missing(exprs))" won't be
> called as you have "exprs = new("matrix")" in the definition of the method.

In an R function

  foo <- function(x=integer()) missing(x)

> f()
[1] TRUE
> f(x=1)
[1] FALSE

'missing' has to do with whether the argument is provided by the user,
not in the function definition.

> 
> So, is
> 
> new("ExpressionSet")
> 
> expected to give an error?

no, no error expected, or seen.

> new("ExpressionSet")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples
  element names: exprs
phenoData
  sampleNames:
  varLabels and varMetadata description: none
featureData
  featureNames:
  fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation:

It helps to have your sessionInfo(); implementations change and it's
hard to know which version you're referring to. Here's mine for the above:

> sessionInfo()
R version 2.9.0 Patched (2009-06-06 r48723)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] tools_2.9.0

Martin
> 
> Best,
> Matthias
>