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 :)
Jose
--
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
UK
I usually put (limited) annotation data in the $genes slot at the
RGlist
stage of a limma analysis. This slot is automatically used in output
functions like topTable()
Jan
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Vinoy
Kumar
Ramachandran
Sent: maandag 11 december 2006 11:02
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] How to add additional annotation column in MA.list
orresults.fit
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......
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