[BioC] microRNA microarray analysis

[J.delasHeras at ed.ac.uk]

Quoting Narendra Kaushik <kaushiknk at Cardiff.ac.uk>:

> I am analyzing two color microarrays with limma but I am getting   
> blank and empty spots as
> differentially expressed genes in topTable. I have made spot files   
> but can't get get rid of them.
>
> Any help will be appreciated.

There are several reasons why you may get blank/empty spots as  
differentially expressed.
First of all, the blank/empty spot may not be empty after all. My  
CRUK22K (cDNA arrays) were like that. When I asked the makers about  
it, as I was worried I had the wrong gene list, they told me that  
after they started printing the arrays they found some cDNAs were not  
reliable (might have been misidentified, or simply lost track of  
them), and they renamed them on teh gene list as "blank", rather than  
something else... I do hope this practice is not common, but it can  
happen!
However, the most common reason is probably that you have a real blank  
spot, with near background intensities (very very low). The signal  
ratios for low intensity spots can be quite high, depending on the  
background correction method used, and may give rise to misleading  
results like these. Do your apparently DE blank/empty spots also have  
a low A value? My guess is yes.

You can simply filter your topTable, eliminating any blank/empty spots  
from the list.

I personally don't use SpotFiles. When I want to highlight spots, I  
make a vector of the unique IDs identifying them, and use that  
instead. I find it more simple/flexible that way.

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

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.