[BioC] Limma: design matrix
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:
>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)
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