[Bioc-devel] initialize method for ExpressionSet

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