[BioC] Undesirable behavior of limma MArrayLM?

[Mark Cowley]

Hi Paul,
you've unearthed the terror that is using numerical ID's as rownames!
As a rule, if I have numerical rownames, then I always refer to them  
using a quoted number - ie a character, eg rma["12356",], or  
programatically using the as.character wrapper, eg:
psID <- 12345
rma[as.character(psID),]

I did not realise the error snuck in at your 2nd line  
(fit2$genes[8961,"ID")

This is an important issue to watch out for, for those using new  
generation affy arrays, where the probesetID's/transcript cluster ID's  
or whatever they're now called are numbers.

cheers,

Mark

On 26/06/2008, at 5:33 PM, Paul Leo wrote:

> 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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>
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