[BioC] duplicateCorrelation with few arrays

[Sergio Barberan]

Hi,

It is possible that my only problem is that I'm trying to use
duplicateCorrelation with few arrays but I just wanted to be sure.

My slides include three replicas of each spot 120 spots apart;
to make sure I'm giving duplicateCorrelation the right input I do:

unwrapdups(MA$genes$Name, ndups=3, spacing=120)

and I do obtain a matrix with identical columns with the replica spots
on it.

My problem is that when I try to calculate:

cor <- duplicateCorrelation(MA,design,ndups=3,spacing=120)

I get several warnings: 1: NaNs produced in: sqrt(dfitted.values)

and I get a correlation of 1.

Right now I do not have two more arrays than the column rank of design,
but I was still trying to get some results; is this the problem or is
there something I'm doing wrong.

Thanks in advance for your help,
Sergio