[BioC] Disorderly duplicate spots

[Yannick Wurm]

Dear List,

I am a graduate student working with the fire ant Solenopsis invicta.
We did some two-color cDNA microarrays that I've begun analyzing with  
limma. But something feels wrong about how I'm doing things: we  
printed whole clones from a ~25,000 clone cDNA library onto our  
microarray. Simultaneously, we sequenced our clones. They assemble to  
~12,000 transcripts. Many are singlets, but some transcripts are  
represented by multiple clones (one transcript is represented by 32  
clones!).

So during analysis, treating each clone as independent feels wrong.  
It means:
	- correcting for 25,000 multiple tests rather than 10,000, thus  
reducing my power;
	- and not taking into account the technical replication we get by  
multiple spots on the array.

The limma manual has a section on Within-Array Replicate Spots. But  
only mentions what to do for people who have a single duplicate of  
every spot on their array.

I'm sure other people have had to deal with this in the past. Do you  
have any pointers?

Thanks & regards,

Yannick


--------------------------------------------
          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
   http://www.unil.ch/dee/page28685_fr.html