Hi! I switched from using R in windows to using it in linux as it seems to be more straight-forward that way. I was about to attempt to normalise my affy cel files using Li and Wong's dChip with widget=T but am unsure how to define my co-variates. I have 8 human chips: 2 X Control, 2 X Treated with LPS, 2 X Treated with LPS+Yeast and 2 X Treated with Yeast Alone. I was thinking of putting 2 co-variates in: LPS and Yeast and then putting in the info as TRUE or FALSE to define how each chip was treated. Would this be totally wrong? I suspect so. Any help here would be greatly appreciated, Mary Logue

if understand you correctly thats exacyly what you want. you have factorial desing. it should look somthing like this array LPS Yeast 1 0 0 2 0 0 3 0 1 4 0 1 5 1 0 6 1 0 7 1 1 8 1 1 with 0 means its not added, 1 that it is. btw, what you get from affy is not dChip. its bioconductors best attempt at reproducing dChip following the papers by li and wong. On Fri, 21 Mar 2003, Mary Logue wrote: > Hi! > > I switched from using R in windows to using it in linux as it seems to be > more straight-forward that way. > > I was about to attempt to normalise my affy cel files using Li and Wong's > dChip with widget=T but am unsure how to define my co-variates. > > I have 8 human chips: 2 X Control, 2 X Treated with LPS, 2 X Treated with > LPS+Yeast and 2 X Treated with Yeast Alone. > > I was thinking of putting 2 co-variates in: LPS and Yeast and then putting > in the info as TRUE or FALSE to define how each chip was treated. > > Would this be totally wrong? I suspect so. > > > Any help here would be greatly appreciated, > > Mary Logue > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >