[BioC] toptable with multiple coefs [was Time course experiment....]

Naomi Altman naomi at stat.psu.edu
Wed Jan 4 04:44:35 CET 2006

Thanks, Gordon.

I think that this is exactly what we need.



At 09:11 PM 1/3/2006, you wrote:
>I give results to many of my collaborators in exactly the same way 
>(except for sorting by gene ID, see below). They like to have all 
>the results in an Excel spreadsheet so that they can play around 
>with it a bit themselves. I use
>   write.fit(fit)
>to create such a file. Does this do what you want?
>Regarding the gene IDs, there isn't a way for limma functions to 
>sort results by gene ID, because there isn't a requirement that the 
>'genes' component of a MArrayLM object contains a column which is a 
>unique probe identifier. Even if such a column does exist, there is 
>no requirement that it has to be called "ID". So limma doesn't have 
>a way to know which column to use to sort by gene ID.
>However with any specific data set, you will know which column is 
>your ID column. So you could use
>  o <- order( fit$genes$ID )
>  write.fit( fit[o,] )
>At 11:38 AM 4/01/2006, Naomi Altman wrote:
>>Just as this discussion got underway, I met with my current 
>>microarray collaborator.
>>She asked that
>>a) The results be sorted by gene id
>>b) all the coefficients and their p-values be printed out to the 
>>same (big) table
>>c) all the gene annotations be added to the table
>>Very timely.

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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