[BioC] Limma
Kim Kulltima
kim.kultima at farmbio.uu.se
Tue Nov 11 13:41:40 MET 2003
Hi!
I have a problem concerning the Limma package, version 1.3.1 and 1.3.2.
I normally run:
RG.median.no.back.w01 <-
read.maimages(files,"genepix",columns=list(Rf="F635.Median",Gf="F532.Median",Rb="F3.SD",Gb="F3.SD"),wt.fun=wtflags(0.1))
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?
Sincerely,
Kim Kultima
-------------------------------------------------------------------
Kim Kultima
Department of Pharmaceutical Biosciences
Division of Toxicology
Uppsala University
The Biomedical Center
Box 594
SE-75124 Uppsala
Sweden
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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