[BioC] limma duplicateCorrelation question

[Gordon Smyth]

Dear Karen,

The design matrix certainly does affect the duplicateCorrelations(), 
so I suspect that you've made a bookkeeping error. Either that or 
your data is artificial and has a some symmetry built into it.

Best wishes
Gordon

>Date: Fri, 1 Dec 2006 16:09:16 -0800
>From: "Karen Vranizan" <vranizan at berkeley.edu>
>Subject: [BioC] limma duplicateCorrelation question
>To: <bioconductor at stat.math.ethz.ch>
>Content-Type: text/plain
>
>The following two commands give me the same result for corfit$consensus:
>
>corfit<-duplicateCorrelation(MA,c(1,1,1,1,1,1),ndups=1,block=(1,1,2,2,3,3))
>
>corfit<-duplicateCorrelation(MA,c(1,-1,1,-1,1,-1),ndups=1,block=(1,1,2,2,3,3))
>
>It seems that the design vector argument doesn't affect the 
>calculations.  Is that correct?  If not, then why is the design 
>vector used here?
>
>Thank you.
>
>Karen Vranizan
>Functional Genomics Lab
>261A Life Sciences Addition
>Mail Code #3200
>UC Berkeley, CA 94720-3200
>
>Phone: 510-642-7520
>Fax:      510-643-2685
>email: vranizan at berkeley.edu