[BioC] Genomic DNA as a reference and limma

[michael watson (IAH-C)]

Hi John

The attributes of any good reference sample are that it is constant
between experiments and that it lights up the majority of spots.  If
your genomic DNA meets these criteria, then there is not a problem.

I myself have analysed data like this.  The main issue is that the
genomic DNA reference tends to be much stronger in intensity than the
RNA sample, so it is useful to avoid saturation in the reference channel
whilst scanning.  

If the assumption that the majority of genes will not be changing, and
that the the average ratio will be 1, is still valid biologically, then
the normalisation methods such as median, loess etc are still valid.

Once you have a good measure for the relative expression of each gene,
limma is a good package to use, and one on which the IAH has
standardised on

Michael Watson
Head of Informatics
Institute for Animal Health,
Compton Laboratory,
Compton,
Newbury,
Berkshire RG20 7NN
UK

Phone : +44 (0)1635 578411 ext. 2535
Mobile: +44 (0)7990 827831
E-mail: michael.watson at bbsrc.ac.uk
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of john seers
(IFR)
Sent: 13 February 2006 15:25
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Genomic DNA as a reference and limma

 
Hello All
 
I have some data using genomic DNA as a reference and I am not quite
sure what the implications are of this are. For instance is limma a
suitable package to analyse this? Would I have to do something extra
with the data?
 
If anybody has any experience of this or can point me to any suitable
documentation I would be grateful.
 
Regards
 
John Seers
 
 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

tel +44 (0)1603 251490 fax +44 (0)1603 255167
e-mail john.seers at bbsrc.ac.uk                         
e-disclaimer at http://www.ifr.ac.uk/edisclaimer/
<http://www.ifr.ac.uk/edisclaimer/>  
www.ifr.ac.uk <http://www.ifr.ac.uk/>    www.foodandhealthnetwork.com
<http://www.foodandhealthnetwork.com/> 
 

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