[BioC] lumi: LumiBatch slots don't match documentation

[Pan Du]

Thanks for pointing out this! Gordon
I will add the description of these two slots in the LumiBatch
documentation. Also I will add them in the summary returns.


Pan


On 10/26/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 19
> Date: Fri, 26 Oct 2007 18:25:21 +1000
> From: Gordon Smyth <smyth at wehi.EDU.AU>
> Subject: [BioC] lumi: LumiBatch slots don't match documentation
> To: "BioC Mailing List" <bioconductor at stat.math.ethz.ch>
> Message-ID: <6.2.5.6.1.20071026182011.01f2b8e0 at wehi.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> LumiBatch objects contain two slots (controlData and QC) which are
> not mentioned on the documentation page help("LumiBatch-class"). Yet
> they don't contain the slot "summary" which is described on the help page.
> 
> What are controlData and QC and how are they used?
> 
> Is summary defunct?
> 
> Gordon
> 
>> library(lumi)
>> a <- new("LumiBatch")
>> slotNames(a)
> [1] 
> "history"           "controlData"       "QC"                "assayData"
> [5] 
> "phenoData"         "featureData"       "experimentData"    "annotation"
> [9] ".__classVersion__"
> 
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=
> English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices
> utils     datasets  methods   base
> 
> other attached packages:
>   [1] 
> lumi_1.4.0           annotate_1.16.0      xtable_1.5-1
> AnnotationDbi_1.0.0
>   [5] 
> RSQLite_0.6-3        DBI_0.2-3            mgcv_1.3-27
> affy_1.16.0
>   [9] preprocessCore_1.0.0 affyio_1.6.0         Biobase_1.16.0
> 
> 
>