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

[Naomi Altman]

A single loop design includes 2 replicates.

  I would do a separate channel analysis as described in the Limma manual 
section 17.

--Naomi

At 02:12 PM 8/19/2005, Claus Mayer wrote:
>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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111