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)
[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.
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:
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