[BioC] Bug in featureNames() in R-2.5.0 / BioC 2.0?

[Martin Morgan]

Philip --

Thank you for the report. This has been corrected, and should appear
as affy version 1.14.1 in the next couple of days.

Martin

"Groot, Philip de" <philip.degroot at wur.nl> writes:

> Hello list,
>  
> While checking my scripts against the new R/BioC versions, I encountered the following unexpected behaviour. Please consider the following peace of code:
>  
> library(simpleaffy)
> x <- ReadAffy()
>  
>> x
> AffyBatch object
> size of arrays=1002x1002 features (14 kb)
> cdf=Mouse430_2 (45101 affyids)
> number of samples=6
> number of genes=1004004
> annotation=mouse4302
> notes=
>
>> featureNames(x)[1:5]
> [1] "1" "2" "3" "4" "5"
>
>> geneNames(x)[1:5]
> [1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
>
> ADDITIONALLY: when I do the following, the output is correct:
>  
> x.norm <- rma(x)
>  
>> featureNames(x.norm)[1:5]
> [1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
>> geneNames(x.norm)[1:5]
> [1] "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   "1415674_a_at"
> Warning message:
> 'geneNames' is deprecated.
> Use 'featureNames' instead.
> See help("Deprecated")
>
>  
> Because of the "deprecated" message, I changed all geneNames() commands in featureNames() commands and hence found this inconsistency. I guess that my assumption is valid that the commands featureNames and geneNames should always obtain exactly the same results, is it not?
> If not, please explain!
>  
> R/BioC is compiled and runnung on the following linux distribution:
> SUSE LINUX Enterprise Server 9 (x86_64)
> VERSION = 9
> PATCHLEVEL = 3
>
> The gcc version used is:
> gcc (GCC) 3.3.3 (SuSE Linux)
> Copyright (C) 2003 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> Regards,
>  
> Dr. Philip de Groot
> Wageningen University
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org