[R] LIMMA: makeContrasts() function

From: Jay Shin <jay.shin_at_pharma.ethz.ch>
Date: Mon 31 Jul 2006 - 20:35:39 EST


Hello,
I am trying to run a makeConstrasts() function to compute eBayes t- test with the following design list (six hybridizations and three samples -in duplicates):

	A   B    C
1	   1   0    0
2 	  1   0    0
3 	  0   1    0
4 	  0   1    0
5  	 0   0    1
6  	 0   0    1

I would like to compare sample "B-C", so when I run:
>contrasts.matrix<-makeContrasts(B-C, levels=design)
it works great!

However, I have B and C stored in as 'member' (e.g. member[1] = B, member[2] = C).
So, when I try to run:
member1<-member[1]
member2<-member[2]
>contrasts.matrix<-makeContrasts(member1-member2, levels=design)

  I get a following error message:
Error in eval(expr, envir, enclos) : object "member1" not found

Can you please help me how I can directly compare the content of the 'member' in makeContrasts() function?
Thank you,
Jay

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