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2009 Mar 13
0
Singal channel spike in controls with custom microRNA slides - Normalization help needed
...9;m working with custom slides(Cy5) and working in the normalization of the
arrays.
I have three arrays (technical replicates).
I have sucesfully normalized the data using vsn, however i would like to
normalize using spike in controls.
My controls are annotated as CTL-1 to x and i would like to do etiher a
normalization by block per array or the mean of all the controls per array.
The gal file is also loaded with all the array structure. Each block
contains spike in controls.
Here is the code:
library(limma)
library(RColorBrewer)
library(vsn)
Cy5 <- "F635 Mean"
Cy5b <- "B635...