[BioC] Triplicate printing and limma

[Brooke-Powell, Elizabeth]

Hi Barry,

Thank you for your help.. I have used this for duplicates, but triplicates
pose a bit more of a problem. Mainly in the organization of them to get even
spacing and different pins. Now maybe limma only really deals with
duplicates, that I don't know. The problem is that while my triplicates are
space 240 features apart I get an error in LimmaGUI. Now I don't know if by
using the command line this will go away or not. I am going to a workshop in
a few weeks and hopefully I can learn command line. It just makes me nervous
is if I re-sort the data files to have the replicates one after another and
do 3 spacing 1 that if the duplicate correlation calculation is actually a
modified calculation that accounts for spatial positioning I might be
actually performing the wrong calculation. I am not sure if that makes
sense?

Liz

-----Original Message-----
From: Barry Henderson [mailto:barry.henderson at ribonomics.com] 
Sent: Friday, September 09, 2005 10:43 AM
To: Brooke-Powell, Elizabeth; BlueFutures at yahoogroups.com;
bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] Triplicate printing and limma

Not an expert but I have done this for a custom array with duplicates.
Limma can deal with replicate spots that are evenly spaced (ndups and
spacing functions in the correlation.  Either all of your duplicates are
adjascent or spaced by some regular number of interveining spots.   I simply
duplicate our array layout.  The top 2 meta rows are identical to the bottom
2 in my case. My cuplicateCorrelation and lmFit lines then look like:
 
correlation <-duplicateCorrelation(limma.nb, design, ndups=2, spacing=2888)
treatmentMeans.fit <- lmFit(limma.nb, design, ndups=2, spacing=2888,
correlation=correlation$consensus.correlation)

 
The limitation of limma at this point is that you can not (or I have not
figured out how to) deal with the intra array duplication at the same time
you want to deal with dye swap.  Or at least that is my take on it as a non
statistician.
 
Barry

	-----Original Message----- 
	From: bioconductor-bounces at stat.math.ethz.ch on behalf of
Brooke-Powell, Elizabeth 
	Sent: Fri 9/9/2005 11:27 AM 
	To: BlueFutures at yahoogroups.com; bioconductor at stat.math.ethz.ch 
	Cc: 
	Subject: [BioC] Triplicate printing and limma
	
	

	Good Morning,
	
	
	
	I am writing to ask some advice. We are presently printing a 39,000
feature
	array and I need some help. We are printing with the triplicates in
the same
	block and I cannot figure out how to get them out of the same block.
It is
	making limma analysis very difficult as the program seems to be
designed to
	analyze printed replicates in different blocks. Can anyone help me
in
	figuring out how to arrange my 96-well plates of oligos and or a get
around
	for limma?
	
	
	
	Thank you for your help,
	
	
	
	Liz Brooke-Powell
	
	
	
	Washington University Medical School,
	
	Department of Molecular Microbiology,
	
	CB#8230, 660 S. Euclid Ave
	
	St. Louis, MO, 63110
	
	
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