Question: duplicate spots
gravatar for David
9.4 years ago by
David860 wrote:
Hi, 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($R) #I try to fit a an object by taking into account duplicate spots (2 spots, spacing=1) fit <- lmFit(mat.vsn, design, ndups=2, correlation=corfit$consensus,weigth=RG$weights[idx,]) 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. thanks david
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