Personally I don't like this kind of behavior  see "#*** and comments...
It will surely catch someone out, will it use a rowname or a  number ,
the joy of variable interpolation!
Do I complain too much or is this worth a fix?

> n<-8963
> fit2[8963,]$genes["ID"]
            ID
8963 106220736               ## ok that's what I wanted
> fit2$genes[8961,"ID"]  #** 
[1] "5050440"		 ## oops!
> test<-fit2$genes
> test[8963,]
[1] "106220736"	## life is sane again, but now I need more caffeine!
> 
> n<-8963
> fit2[n,]$genes["ID"]
            ID
8963 106220736
> fit2$genes[n,"ID"]  ### Works as I would expect AGAIN
[1] "106220736"
> test<-fit2$genes
> test[n,]
[1] "106220736"
> 
> fit2[8963,]$genes["ID"]
            ID
8963 106220736
> fit2$genes[8961,"ID"]
[1] "5050440"
> fit2$genes["8961","ID"]  # Oh yes... now I get it!
[1] "5050440"
> fit2$genes[n,"ID"]
[1] "106220736"


> class(fit2)
[1] "MArrayLM"
attr(,"package")
[1] "limma"
> sessionInfo()
R version 2.7.1 RC (2008-06-16 r45949) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:
[1] limma_2.14.5
>


Cheers
Paul



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