[BioC] A question about within-array replicates with limma

Wei Xu xuwei3 at msu.edu
Tue Mar 11 18:03:01 CET 2008

Hi, all,

I have question about the within-array replicates analysis with limma.

The replicates for each spot in my cDNA microarray are irregular-spaced. 
There are 3 replicates for each spot, which are randomly distributed in 
the array. When I entitled "irregular=True, ndup=3, spacing=1", I 
thought the space will be counted automatically based on gene IDs. 
However, in the output table, I can still find some genes listed twice 
with different values (i.e. B values, p-values, etc). Did I do anything 
wrong with that? I went through lots of examples online, and most 
samples with replicated spots are regulated spaced. Could you please 
tell me what I am supposed to do with this kind of problem? I really 
appreciate it. Thanks.


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