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 Val?rie -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 896 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040305/2d4dfb06/attachment.bin

> 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 ? Woops, it's a bug. Thanks for pointing this out. I'll fix it. Gordon > Thanks > Val?rie