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

[r.athanasiadou]

Hi Rob!
Is the number of rows the same in each table?In other words do both the
tables contain the same genes/spots?

Is the identifier of the second table eg I6481 unique (in other words no
matter the second part of the identifier in the Top Table, is the first part
unique and enough to identify the spot)?

If the answer in both questions is yes then just do 
pos<-order(toptable[,5])
TopTable2<-toptable[pos,]

And 
pos<-order(geneinfotable[,<the column that has the gene identifiers>])
geneinfotable2<-geneinfotable[pos,]


Now both the tables have the spots in the same order!

Niki
ICB
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University of Edinburgh
Edinburgh, EH9 3JR
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UK

tel:(0044)0131-6507072
fax:(0044)0131-6505379
R.Athanasiadou at sms.ed.ac.uk


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of RS Illingworth
Sent: 03 May 2007 15:47
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Using Top Table to extract gene info from additional
tablewithin

Hi

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 
avail!!

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

Any help would be greatly appreciated.

Thanks

Rob Illingworth

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