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
At 11:26 PM 18/09/2003, Jason Skelton wrote:
>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 ?
You need to type
library(modreg)
By the way, the fact that you are having this problem shows that you
are
using an old version of R and a version of limma somewhere between the
last
official release and the current development version. Updating either
R or
limma to the latest version will solve the problem permanently.
>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 ?
It doesn't matter which way around you do it as long as you know and
interpret the results the right way. I always do it so that
upregulation in
the red channel corresponds to positive log-ratios.
Gordon
>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
