[BioC] Analysing a timecourse/loop experiment without replication with limma

[Claus Mayer]

Dear all!

I am trying to analyse a timecourse experiment using two-color 
microarrays with limma. There are 5 timepoints compared in a 
loop-design, i.e 1 vs 2, 2 vs 3,…, 4 vs 5, 5 vs 1. This experiment is 
supposed to be repeated 3 more times (with independent samples) but my 
collaborators were interested
to see the results for this first set of experiments before they 
hybridise the rest. I have put the data into limmaGUI and chose the 4 
first present comparisons (2 minus 1, 3 minus 2, 4 minus 3 and 5 minus 
4) as parameters. When I try to fit the model I get an error message 
saying “Error in colSums(fit$effects(fit$rank+1):narrays,]^2 ‘x’ must be 
an array of at least two dimensions”.

At first I thought I just ran into a singularity problem caused by the 
lack of repitition (although I had originally thought with each sample 
being present twice that should be no problem). But then I tried the 
same thing with a completely different data set, that had the identical 
design (with 4 instead of 5 timepoints). In this case everything went 
fine, which indicates something else must have been wrong with my first 
analysis.

So I went pack and just changed the targets file for my original data 
set and now claimed that each array was just comparing a treatment with 
control. The reasoning was to check whether there was anything wrong the 
data files themselves. With this new (and completely wrong) design I was 
able to run the analysis, which means that there is nothing obviously 
wrong with the data.

I probably have overlooked something very obvious or I am just doing 
something stupid but perhaps one of you can put me in the right direction.

Any helpful comments appreciated.

Thanks,


Claus

-- 
***********************************************************************************
 Claus-D. Mayer                       | http://www.bioss.ac.uk
 Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
 Rowett Research Institute            | Telephone: +44 (0) 1224 716652
 Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349