[BioC] reading txt files, plots and linear models

[Matthew Hannah]

Jamilia,

If you did this - 
data <- ReadAffy() 
eset <- rma(data) 
write.exprs(eset,file="myresults.txt") 

Then you can get the data back in by - 
rma <- read.table("C:/your directory/myresults.txt", header=T)

You can then get a boxplot by
boxplot(rma)
boxplot(rma[,1]) #to select a specific column

a scatterplot
plot(rma[,1], rma[,2], pch=".")

If you mean you want boxplots of the CEL files before rma then 
data <- ReadAffy()
boxplot(data)


If you have an exprsset
eset <- rma(data)

Then to get a boxplot of this you could try (example with 6 chips)
x <- exprs(eset)
boxplot(x[,1], x[,2], x[,3], x[,4], x[,5], x[,6])

You might find also the following useful as you can add phenodata (exp,
time, replicate etc..) as covariates which you can then subset on later 
eg: eset$experiment
data <- ReadAffy(widget=T)

I'm also new to BioC/R but find the html help for the packages as well 
as vignettes useful.

Good luck
Matt