[Bioc-devel] initialize method for ExpressionSet

[Matthias Kohl]

Hi Martin,

sorry, my fault ...

Best,
Matthias

Martin Morgan schrieb:
> 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
>>
>>     
>
>   

-- 
Dr. Matthias Kohl
www.stamats.de