[BioC] Limma

Kim Kulltima kim.kultima at farmbio.uu.se
Tue Nov 11 13:41:40 MET 2003


I have a problem concerning the Limma package, version 1.3.1 and 1.3.2.
I normally run:
RG.median.no.back.w01 <- 

The Rb=F3.SD and Gb=F3.SD are just columns with 0 zeros in.

However in the new packages for the help file for ma.images it says:

#  Read all .gpr files from current working directory
#  and give weight 0.1 to spots with negative flags

## Don't run:
files <- dir(pattern="*\\.gpr$")
RG <- read.maimages(files,"genepix",wt.fun=wtflags(0.1))
## End Don't run

#  Read all .spot files from current working director and down-weight
#  spots smaller or larger than 150 pixels

## Don't run:
files <- dir(pattern="*\\.spot$")
RG <- read.maimages(files,"spot",wt.fun=wtarea(150))
## End Don't run

Do you know what the problem is, and how do I read in my data now?


Kim Kultima

Kim Kultima
Department of Pharmaceutical Biosciences
Division of Toxicology
Uppsala University
The Biomedical Center
Box 594
SE-75124 Uppsala
Phone +46-18-4714254
Fax +46-18-4714253
Email: Kim.Kultima at farmbio.uu.se
Home Page http://www.farmbio.uu.se/tox/index.html
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