[BioC] kooperberg syntax

[michael watson (IAH-C)]

library(limma)
?kooperberg

Gives the example code as:

genepixFiles <- dir(pattern="*\\.gpr$")      
read.series(genepixFiles, suffix=NULL, skip=26, sep="\t") 
layout <- getLayout(get(genepixFiles[1]))
RGmodel <- kooperberg(genepixFiles, layout=layout) 

i.e. you need to use read.series to read in your data.

Mick
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
scholz at Ag.arizona.edu
Sent: 22 August 2005 17:28
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] kooperberg syntax


Hi,

R2.1.1
Windows XP
absolute beginner

I'm having problems using the Kooperberg normalization method. Here's a
screenshot of my error, along with some background code:

----------------------------
> targets <- readTargets("Targetdyeswap.txt")
> RG <- read.maimages(targets$FileName, source="genepix")

Read B115_R480_G430.gpr 
Read B116_R480_G430.gpr 

> RG$genes <- readGAL("MOB-1-3.anno.gal")
> RG$printer <- getLayout(RG$genes)
> RGmodel <- kooperberg("B115_R480_G430.gpr", layout=RG$printer, 
> fg="mean",
bg="median")

Error in get(x, envir, mode, inherits) : variable "B115_R480_G430.gpr"
was not found
------------------------------

Why is my filename now being viewed as a variable? Thanks in advance.

Matt

---------------------------------------------
College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor