[BioC] gls.series error ?

[Valerie Cognat]

Hi,

I use limma to analyse my dye swap. I have 3 replicates with a spacing 
of 1152.
When I use the gls.series function I obtain a very small correlation.
fit <- gls.series(data,design=flip,ndups=3,spacing=1152)
fit$cor : 0.1937247
But if I use the dupcor function
cor <- dupcor.series(data,design=flip,ndups=3,spacing=1152)
cor$cor = 0.6515627
if I "miss" the spacing
cor <- dupcor.series(data,design=flip,ndups=3,spacing=1)
cor$cor = 0.1937247

The gls.series function don't use the spacing argument to calculate 
correlation ?

Thanks

Valérie





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