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

[Jean Yee Hwa Yang]

Hi Charles,

maTwoSamples were design to swap cDNA Dye Swap Experiment from target
files coming from data bases with one one channel information per line.
In the swirl example, it will be looking for the following input
E.g.

TargetName	Slides		Dyes	PrintDate	Names
swirl		slide81		3	2001/9/20	swirl.1.spot
wildtype	slide81		5	2001/9/20	swirl.1.spot
swirl		slide82		5	2001/9/20	swirl.2.spot

I will update the documents and make this clearer.  For the mean time to
calculate various statistics from dye swap experiment, you will need to
specified the dye flip manually.  

There are two alternative options:
A)
## Normalized and extra your data
M <- maM(manorm(swirl))

## Swap the Dye manually
swirl.M <- sweep(M, 2, c(-1, 1, -1, 1), FUN="*")

## Calculate the various statistics using widget (option (a))
## Select from the widget the statistics you like to calculate,

widget.Stat(swirl.M, outputName="myres")   

## or use maStat, here you can write your own functions in addition to the
## mean, t-stat and B-stat that is provided (option (b)).

res <-  maStat(X, funNames=c("meanFun", "ttestFun"))
   
## use stat.gnames to select the top genes.

stat.gnames(res[,"meanFun"], maGeneTable(swirl), crit=30)

B) Use the package limma 
library(limma)
M <- maM(maNorm(swirl))
design <- c(-1,1,-1,1)   

## Fit a linear model
fit <- lm.series(M, design)  

## t-stat can be obtain from
fit$coef

## B-stat (empirical Bayes)
eb <- ebayes(fit)

## Generate 30 top genes using
toptable(number=30, genelist=maGeneTable(swirl), fit=fit, eb=eb)

Hope this help.

Cheers

Jean

On Fri, 30 May 2003, White, Charles E WRAIR-Wash DC wrote:

> 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:
> 
> 
>   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
>