[BioC] duplicate spots

David martin vilanew at gmail.com
Mon Jun 7 16:16:08 CEST 2010

I'm using single channel (Cy5) arrays.

i# have background corrected the arrays, removed the Cy3 components from 
the RG object. RGfinal corresponds to a subset of the genes of interest 
(controls are removed and empty spots)

#So i apply a vsn normalisation
mat.vsn <- vsnMatrix(RG.final$R)

#I try to fit a an object by taking into account duplicate spots (2 
spots, spacing=1)
fit <- lmFit(mat.vsn, design, ndups=2, 
ebayes <- eBayes(fit)

#I compute DE genes
a <- topTable(fit2, coef=1, adjust="BH",number=100)

Now i want to retrieve the normalized values from this genes and draw 
the heatmap.
The problem is that mat.vsn  still contains the duplicate spots, so 
extracting the values from the normalized matrix is not easy.

How can i retrieve the normalized valued across all conditions for a 
particular gene without retrieveing the duplicated spots ?? The fit 
object would only return the conditions stated in design but not for all 
arrays individually.



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