[BioC] LumiBatch: problem when renaming samples

[Pan Du]

Hi Cei,

Thanks for reporting the bug. As Wolfgang mentioned, we just used  the
default "sampleNames<-", as a result, some of the colnames of additional
elements were not changed. I have updated the code. The updated version is
1.7.2, which should be available in the next few days.
Thanks!


Pan


On 5/6/08 7:43 AM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:

> Dear Cei, Pan,
> 
> thanks for reporting this. It appears indeed that it is a bug in the
> lumi package: the "LumiBatch" class inherits from Biobase's "eSet", but
> has additional slots, and one of the ugly effects is that the
> sampleNames are stored in multiple places.
> 
> However, the "sampleNames<-" method is inherited from eSet without
> modification, so only updates those two places where they are in any
> eSet, but not the other, LumiBatch-specific occurences, leaving the
> object in an inconsistent state, which confuses the (LumiBatch-specific)
> "["-method.
> 
> Best wishes
> Wolfgang
> 
> 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
> 
> Cei Abreu-Goodger a écrit 05/05/2008 18:10:
>> 
>> Hi all, this seems like a bug to me, but please correct me if I'm doing
>> something wrong. If I rename the samples of a LumiBatch object, I can no
>> longer subset them by name (with numbers it still works). Here's an
>> example, followed by my sessionInfo.
>> 
>> library(lumi)
>> data(example.lumi)
>> 
>> # This works
>> example.lumi[,sampleNames(example.lumi)]
>> 
>> # But if I rename the samples
>> sampleNames(example.lumi) <- gsub("0","",sampleNames(example.lumi))
>> 
>> # It no longer works
>> example.lumi[,sampleNames(example.lumi)]
>> 
>> #Error in example.lumi[, sampleNames(example.lumi)] :
>> #  subscript out of bounds
>> 
>> 
>> ==================================================
>>> sessionInfo()
>> R version 2.7.0 (2008-04-22)
>> i386-apple-darwin8.10.1
>> 
>> locale:
>> C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  tools     utils     methods
>> [8] base
>> 
>> other attached packages:
>> [1] lumi_1.6.0           mgcv_1.3-30          affy_1.18.0
>> [4] preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.0
>> 
>> 
>