[BioC] Searching for data in data.frames

Stephen Henderson s.henderson at ucl.ac.uk
Fri Apr 21 16:03:13 CEST 2006

Have you tried


Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
J.delasHeras at ed.ac.uk
Sent: 21 April 2006 14:55
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Searching for data in data.frames

This may be a very basic question, but I am looking in the R manual and 
I haven't found the right function... and I am sure it must exist 
already. So I apologise in advance if I seem to be blind or missing 
something! :)

What I am after is very simple. I am using Limma and I have a number of 
data frames (RGList, MAList, MArrayLM...). Sometimes I just want to 
locate the data for a particular gene, or where a particular value for 
M occurs, etc.

I want to find, for instance, all occurrences of "COL6A3" in RG$genes, 
and return the position of those occurrences, for instance 345, 7840, 
15003. Then I can use that information to give me the foreground 
intensities corresponding to that gene for any given slide.

I came across the function "subset" which seems like it would serve my 
purpose (or could be adapted to serve my purpose), but I get errors no 
matter what I do...

I appreciate this must be a pretty basic question, but... I have spent 
the last hour searching for this and so far no luck. I was going to 
just write a simple search function, but there must be already a 
function already defined.



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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