---------- Forwarded message ----------
From: Harikrishnadhar <hari.bombex@gmail.com>
Date: Mon, Aug 30, 2010 at 3:36 PM
Subject: template matching
To: Bioconductor@stat.math.ethz.ch



Dear All,

I am doing my analysis for time series data and have to perform template
matching.

I am new to this concept and need some help to proceed further

Here are the details of my analysis:

I have 7000x 82 matrix in which rows are the genes and col are samples
respectively.

I have to define templates using 6 different combination for which have used

the following code;

templates <- permutations(3,6,c(-1,0,1),repeats=T)

comb1<-c (1,2,3,4)
com2 <- c (5,6,7,8)
com3 <- c (9,10,11,12)
com4 <- c(13,14,15,16)
com5 <- c(17,18,19,20)
com6 <- c(21,22,23,24)
com7 <- c(25,26,27,28)

To get the 729 profiles for the templates using permutation code is as
follows

profile <- matrix(0,nrow=729,ncol=82)

for (i in 1:729){

 profile[i,hf1hr.cols] <- templates[i,1]
 profile[i,hf6hr.cols] <- templates[i,2]
 profile[i,hf24hr.cols] <-templates[i,3]

 profile[i,cho1hr.cols] <- templates[i,4]
 profile[i,cho6hr.cols] <- templates[i,5]
 profile[i,cho24hr.cols] <- templates[i,6]
}


once i run the above code I have 729 x82 profiles.

 I have to calculate correlation of each gene with each profile. Should have
a 7000 X 729 size matrix.
 Then have to find for each gene,the profile with maximum absolute
correlation and use that number for that gene.I should end up with 7000 X 1
sized profile assignment.


I am struck in between my analysis please help with this!!!!!!!!!!!!!!!!!!!!

It would be greatly appreciated if I get some suggestions,code,or links.

Have a great day






-- 

Thanks
Harikrishnadhar Sonnenahalli







-- 

Thanks
Harikrishnadhar Sonnenahalli

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