[BioC] limma normalization
Jason Skelton
jps at sanger.ac.uk
Thu Sep 18 15:26:45 MEST 2003
Hi
trying to use limma with my own genepix data
have a problem when I try to use the following commands:
> dictyMA <- normalizeWithinArrays(DictylimmaRG,
layout=dictylimmalayout, method="printtiploess")
Error in residuals(loess(y ~ x, weights = w, span = span, na.action =
na.exclude, :
couldn't find function "loess"
> dictyMA <- normalizeWithinArrays(DictylimmaRG, dictylimmalayout)
Error in residuals(loess(y ~ x, weights = w, span = span, na.action =
na.exclude, :
couldn't find function "loess"
Any ideas ?
Also for the design matrix
e.g design <- c(-1,1,-1,1)
I know the negative numbers are dye swaps but does it assume your normal
dye orientation is a certain way around e.g green/red OR red/green for
the positive numbers ?
and therefore the negative numbers(dye swap) is just the reverse or
does it actually matter atall ? (hope that makes sense)
presuming of course that -1, 1 correspond to the order in which you have
read them into limma in the first place ?
thanks
Jason
--
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA
Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919
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