[BioC] toptable missing ProbeId/ documentation question

[Björn Usadel]

Hi James,

double stupid me.
Firstly I do use 2. 4.13 (even though I abuse it by running it on R 2.2.0)
and secondly yes you are completely right topTable does extract the 
ProbeId, it was only that toptable is attached to the same help file.

But since the users' guide only refers to topTable, I guess this is 
perfectly ok. (One shouldn't use toptable to start with)

Otherwise I guess I just volunteered myself for helping in changing the 
documentation since I brought this up.

Cheers,
Björn


> Hi Björn,
>
> Ignore my last email - I don't even have R-2.2.X on my computer 
> anymore, so I got the most recent version for R-2.3.0.
>
> Anyway, the problem here is that you are calling toptable() instead of 
> topTable(). The latter will correctly extract the genelist from your 
> fit object.
>
> Best,
>
> Jim
>
>
>
> Björn Usadel wrote:
>
>> Dear List,
>>
>> Sorry for posting a very minor thing or if this has been posted already,
>>
>> using limma 2.2.13
>> I don't get ProbeIDs back when  calling toptable
>>
>> toptable(fit,num=1)
>>              M        t      P.Value    adj.P.Val        B
>> 22488 13.32117 197.5873 1.039258e-15 7.791015e-13 23.66308
>>
>> It does work though when calling
>> toptable(fit,num=1,genelist=fit$genes)
>>              ID        M        t      P.Value    adj.P.Val        B
>> 22488 267388_at 13.32117 197.5873 1.039258e-15 7.791015e-13 23.66308
>>
>> This is no problem whatsoever, but help toptable states
>>
>> "genelist: data frame or character vector containing gene information.
>>           If not specified, this will be taken from the 'genes'
>>           component of 'fit'."
>> (I hope my docu is also up to date as well)
>>
>> and genelist is set to NULL by default.
>> Furthermore nowhere in toptable is fit$genes referenced (at least I 
>> coudln't find it)
>>
>> a possible fix  which works for me with my limited datasets but I 
>> have no clue about the internals of the fit object:
>>
>> if (is.null(genelist))
>>     +++genelist<-fit$genes
>>         ---tab <- data.frame(M = M[top])
>>     ---else {
>>         if (is.null(dim(genelist)))
>>             tab <- data.frame(ProbeID = I(genelist[top]), M = M[top])
>>         else tab <- data.frame(genelist[top, , drop = FALSE],
>>             M = M[top])
>>     ---}
>>
>> alternatively one could just change the docu of toptable.
>>
>> This is really only an extremly minor thing, but might possibly lead 
>> to confusion.
>>
>>
>> Kind regards,
>>
>> Björn
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>