[BioC] background correction

[Jenny Drnevich]

Hi Yanju,

'plotDensities' plots the log2 of the R and G values, and log2 values of 
positive values less than 1 are negative.

Jenny

At 09:06 AM 11/28/2006, yanju wrote:
>Dear all,
>
>As read from the instruction of backgroundCorrect in limma, the  method
>"half",  "minimum",  "edwards" and so on are all designed to produce
>positive corrected intensities.  My code is as follows:
>
>     rgc<-backgroundCorrect(rg, method="half")
>     plotDensities(rgc)
>
>After I plot the graph of Density-Intensity after this backgroud
>correction, I found there is still some part of curve with the negative
>intensity. Why is it like that?? I try minimun also, the result is
>similar with negative intensity. I dont know how to explain it.
>Expecting your reply.
>
>Regards,
>Yanju
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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