[BioC] Using Top Table to extract gene info from additional table within

RS Illingworth s9902201 at sms.ed.ac.uk
Thu May 3 16:47:05 CEST 2007


I am reliatevely new to R and BioC and have so far been using the 
package limma to analyse my microarray data. I have got to the stage 
where I have some interesting features and want to use the respective 
IDs of these to extract gene data from additional tables within R.

Top table data:

Block Row Column               ID                   Name        M       
  A        t      P.Value    adj.P.Val        B
16415    28   9     15   I6481_cpg298I7 13_108590257-108591866 3.761146 
12.28307 23.07024 1.418257e-16 4.068837e-12 27.90629

Gene info table:
V1 V2     V3     V4       V5   V6    V7              V8               
V9    V10
1 I1  1 828862 830900 function 68.2 0.717            <NA>             
<NA>   <NA>
2 I2  1 847313 850747 function 69.9 0.717 ENSG00000187634  
850393:870375:1 SAMD11

The problem is neither contains exactly the same data in the same 
order, and the IDs in the Top table are extended relative to those in 
the 2nd table eg I6481_cpg29817 in the Top table is simply I6481 in the 
genes data table. So far I have tried various looping grep scripts to 
use the IDs from one table to give me positions in the other - to no 

I think this is probably a fairly trivial problem, but I am starting to 
loose hair over this!!

Any help would be greatly appreciated.


Rob Illingworth

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