[BioC] LumiBatch: problem when renaming samples

[Wolfgang Huber]

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
> 
>