[BioC] How to add additional annotation column in MA.list or results.fit

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Mon Dec 11 11:39:35 CET 2006

Quoting Vinoy Kumar Ramachandran <vinoydna at gmail.com>:

> Dear Limma Users,
> I have a additional text file with edited annotation (two columns (1) Gene
> Id and (2) Edited annotation), i like to add the edited annotation to the
> MA.list or the results.fit. Can anyone suggest me how to do this.
> thanks in advance
> with regards,
> Vinoy......

You can add "stuff" to an MAlist (MA) simply by making a new component  
in it: MA$stuff<-stuff

What I normally do is use 'topTable' applied to all spots, to give me  
the FDR, M values etc. I do that with all the comparisons I have in my  
experiment. Then I order them all as in my gene list, and create a  
large table with all the gene information, IDs, annotation, GO when I  
have it, chromosomal location, etc... and then the ordered topTable  
results... with M values, the corrected P values... and any other  
thing I may want to add. Then this "master table" is very useful to  
compare the behaviour of a gene across experiments, make plots, etc...

You don't need to add anything to an MAlist. Although if you want to  
you can. All you need is to have your annotation IDs etc somewhere, in  
teh same order as the genes in your RG and MAlist... then you can call  
them up as you need.

I am sure others will have more "technical" comments. But this is what I do :)


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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