[BioC] Treatment vs. Control in cDNA Dye Swap Experiment

[White, Charles E WRAIR-Wash DC]

I'm trying to use maTwoSamples but I don't understand the parameters.
Assistance would be appreciated. Using the example swirl data, I'm doing the
following:

{rm(list=ls(all=TRUE))}
> library(marrayInput)
> swirl.layout <- read.marrayLayout(fname = "fish.gal", ngr = 4, ngc = 4,
nsr = 22,
+                                   nsc = 24, skip = 21,ctl.col = 4)
> ctl <- rep("Control", maNspots(swirl.layout))
> ctl[maControls(swirl.layout) != "control"] <- "N"
> maControls(swirl.layout) <- factor(ctl)
> swirl.targets <- read.marrayInfo("SwirlSample.txt")
> swirl.gnames <- read.marrayInfo("fish.gal",info.id = 4:5, labels = 5, skip
= 21)
> datadir <- getwd()
> fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\."))
> swirl<- read.Spot(fnames, path=datadir,
+                   layout = swirl.layout,
+                   gnames = swirl.gnames,
+                   targets = swirl.targets)
[1] "Reading c:\\...\\Demo/swirl.1.spot"
[1] "Reading c:\\...\\Demo/swirl.2.spot"
[1] "Reading c:\\...\\Demo/swirl.3.spot"
[1] "Reading c:\\...\\Demo/swirl.4.spot"
> library(marrayNorm)
> swirl.norm <- maNormMain(swirl)
> swirl.targets
Object of class marrayInfo. 

  maLabels # of slide        Names experiment Cy3 experiment Cy5      date
1       81         81 swirl.1.spot          swirl      wild type 2001/9/20
2       82         82 swirl.2.spot      wild type          swirl 2001/9/20
3       93         93 swirl.3.spot          swirl      wild type 2001/11/8
4       94         94 swirl.4.spot      wild type          swirl 2001/11/8
  comments
1       NA
2       NA
3       NA
4       NA

Number of labels:  4  
Dimensions of maInfo matrix:  4  rows by  6  columns

Notes: 
SwirlSample.txt
> # swap dye posiions
> library(marrayTools)
> maTwoSamples(targetfile=swirl.targets, normdata=swirl.norm, Trt='swirl',
Ctl='wild type', targetID = 3, slidesID = 2, dyesID = 4, RedID = 5, path =
".", output = TRUE)
Error in readLines(con, n, ok) : `con' is not a connection
Error in maInfo(read.marrayInfo(targetfile)) : 
	Unable to find the argument "object" in selecting a method for
function "maInfo"
>

Charles E. White, Biostatistician
Walter Reed Army Institute of Research
503 Robert Grant Ave., Room 1w102
Silver Spring, MD 20910-1557
301 319-9781
WRAIR Home Page: http://wrair-www.army.mil/