[BioC] random positioning of duplicate spots

[Peder Worning]

Hi Vishal,

One way to do this is to use the probe IDs as names of your data points.
I don't know how your system is set up, but I'll show how I summarize by
name without changing the original order of the spots:

mywtfun <- function(exclude.flags=c(1,2,3,4,5,6,7)) 
function(obj) 1-(obj$Flag %in% exclude.flags)
                    
RG.MDA <- read.maimages(file.MDA, source="imagene",
names=target.MDA$Barcode, wt.fun=mywtfun(c(1,2,3,4,5,6,7)),
columns=list(f="Signal Mean",b="Background Median")) 

rownames(RG.MDA) <- RG.MDA$genes[,6]

Cy3.channel.MDA = RG.MDA$G

expression.matrix.MDA <-
apply(Cy3.channel.MDA,2,function(v){tapply(v,names(v),
function(x){median(x,na.rm=TRUE)})})

I use the median of the replicated spot rather than the mean.

I hope it can be of some use and that Outlook doesn't break my lines in
silly places.

Good luck

Peder

Best regards 

Exiqon A/S

 Peder Worning, Ph.D.

Senior Scientist, Biomarker Discovery

Telephone: +45 45650457 
Telefax: +45 45661888  
E-mail: pwo at exiqon.com

 Bygstubben 3 
DK-2950 Vedbaek 
Denmark 
www.exiqon.com 

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-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Vishal
Thapar
Sent: Tuesday, May 05, 2009 7:45 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] random positioning of duplicate spots

Dear List,

I had posted earlier about my problem but didn't get any response that
could
help so I am seeking your help again.

I have duplicate spots on my nimblegen array that are position
randomized so
there is no order to their placement. In Limma when we call the
duplicateCorrelation() function, it requires that the duplicate spots
have
some order to them, like they are either adjacent or they are on upper
and
lower halves of the array. In this case, can someone please help me
about
how to go about analyzing these spots?

I really appreciate your input.

Sincerely,

Vishal

Code:

corfit=duplicateCorrelation(ma.quantile, ndups=2)

This gives me a negative corelation of -0.08 the reason being that the
spots
are randomized. Is there a solution to this?

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