[BioC] Question about affy

Mary Logue marylogue at hotmail.com
Fri Mar 21 16:29:00 MET 2003


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

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