Hi all,

I would like to conduct a time-course analysis using the limma package on my
chip data (run as dual-color). I have two classes/groups with 8 subjects in
each. Each 'experimental unit' has been measured at three different time
points.
However, I already have all the data as lowess normalized log-ratios =>
log2(Hy3/Hy5).  How do I read in my txt-file with my log2 ratio data into R?
And how do I define a vector/data frame?

I have arranged the data  so I have probe ID in the first column (row 2 to
200) and individual slide data in the following columns (that is, slide 1
data in column 2, and slide 2 data in column 3 and so on...). I have 48
slides in total.

The main question I want to answer is which genes are differentially
expressed between the two groups of subjects - at time point 1, 2, and 3,
respectively.

Cheers,
Peter

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