[BioC] Limma: design matrix

Naomi Altman naomi at stat.psu.edu
Fri Jan 23 20:14:50 CET 2009

I cannot speak for the experience of others, but some small 
experiments we did with Agilent arabidopsis arrays with 2 arrays per 
slide did not find a slide effect.  We did find a batch effect - i.e. 
arrays run in a batch are more similar than arrays in different 
batches.  But arrays within slide did not appear to be more similar 
than arrays within batch.

Regarding the duplicate spots - just sort the genes by geneId before 
analysis and use spacing=1.  The effect of spot duplication is 
usually much larger than the effect of position on the array.


At 01:44 PM 1/23/2009, Yolande Tra wrote:

>Hi all,
>I have an unusual microarray design. The experiment is meant to 
>compare two conditions. We have 4 slides of microarrays: all four 
>considered as biological replicates. However, one slide contains 2 
>replicate arrays (we named top and bottom). These two come from the 
>same culture. The design was made this way for frugality. So in 
>total we have 8 samples. I read the limma user guide and there was 
>no example of such design. There are duplicate spots in each array 
>but in random fashion so there is no way to compute the 
>duplicateCorrelation command. I wonder how would I build the design. 
>Any help is appreciated.
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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