[BioC] dupcor.series

[Gordon Smyth]

At 12:44 AM 16/03/2004, Jason Skelton wrote:
>Hi Gordon
>
>I've received and error message with limma that I haven't come across before
>but I only receive it with data that has been normalised between arrays:
>
>cor <- dupcor.series(NWAresults$M, design, ndups=2, spacing=840)
>works fine but if I try:
>
>
>nbaResults <- normalizeBetweenArrays(NWAresults)
>then:
>cor <- dupcor.series(nbaResults$M, design, ndups=2, spacing=840)
>
>It returns:
>
>*Error in chol(dinfo) : the leading minor of order 2 is not positive
>definite.*

I've never seen this error either. What version of R/limma are you using? 
What do you see if you type

summary(nbaResults$M)?

>there are only two slides in this particular experiment could this be
>part of the problem ?

It's probably part of the problem, but we often use dupcor.series on just 
two arrays without any problems. Give me more details of your version etc 
and we will follow it up. I am guessing that you have a lot of missing 
values in your data.

Gordon

>Thanks
>
>Jason
>
>--
>--------------------------------
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute