[BioC] reading txt files, plots and linear models

[Jamila Ahdidan]

Hi all,
I'm still in trouble with reading data from a text
file. I worked on CEL files and run the rma function
on them. Then it saved the results as a test file.
Now, I want to look at the plots (scatter and
boxplot), but I don't want to do them one by one. I
know that there must be an easy way to get all the
plots. Could anyone help me with that.

Then, I wanted to look at the differentially expressed
genes using th elinear model discribed in chapter 7.2
of the limma notes on linear models, but I don't
understand how the model.matrix function works and
what "~ -1+factor(c(...)))" means. More precisely, I
don't know how I can use it with my data. I have 3
different microarray data that I want to compare. Each
microarray is a time serie of 6 time points. I don't
know how I should write my vector. The way I wrote it
seemed ok, but it gave me NA all the way. Why?

I thought BioConductor was supposed to be easy to use,
but I'm getting lost because I don't know what I can
do with it and then how to do it. Is there a
documentation covering the ploting part and how to
look for differentially expressed genes?

I know it's many questions, but I really need to
understand and learn how to use this very usefull
tool.

Thanks a lot in advance,
Jamila