[BioC] limma normalization

[Jason Skelton]

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