[BioC] Triplicate printing and limma

Barry Henderson barry.henderson at ribonomics.com
Fri Sep 9 17:43:06 CEST 2005

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.

	-----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 
	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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