[BioC] random positioning of duplicate spots

Naomi Altman naomi at stat.psu.edu
Wed May 6 01:31:37 CEST 2009

I always sort by probename, which makes the spots adjacent in the 
data matrix.  )f course, this
destroys the spatial correlation, so if you plan to do some spatial 
adjustment, you should do it first.


At 01:45 PM 5/5/2009, Vishal Thapar wrote:
>Dear List,
>I had posted earlier about my problem but didn't get any response that could
>help so I am seeking your help again.
>I have duplicate spots on my nimblegen array that are position randomized so
>there is no order to their placement. In Limma when we call the
>duplicateCorrelation() function, it requires that the duplicate spots have
>some order to them, like they are either adjacent or they are on upper and
>lower halves of the array. In this case, can someone please help me about
>how to go about analyzing these spots?
>I really appreciate your input.
>corfit=duplicateCorrelation(ma.quantile, ndups=2)
>This gives me a negative corelation of -0.08 the reason being that the spots
>are randomized. Is there a solution to this?
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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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