[R] Please help....normalization by the median of some control genes

[Rui Barradas]

Hello,

I'm not sure I understand what you want. You want the medians to be 
"similar"? Why not equal?
(The code below assumes ids represent genes.)


d <- read.table(text="
         id1    id2    id3
control1    0.8    0.7    0.6
control2    0.6    0.2    0.4
probe1        0.3    0.2    0.5
probe2        0.4    0.9    0.7
probe3        0.6    0.7    0.4
", header=TRUE)
d

d.new <- sapply(d, function(x) x - median(x))

The medians are now all equal to zero.

Hope this helps,

Rui Barradas

Em 23-08-2012 13:37, David Lyon escreveu:
> Can someone show me some code to do normalization by the median of some control genes for the example below?
>
> Many Many Thanks in advance
>
>
>
> This strategy selects a subset of genes (called “control genes”) and makes the median of their data distribution similar across arrays.
>
>          id1    id2    id3
> control1    0.8    0.7    0.6
> control2    0.6    0.2    0.4
> probe1        0.3    0.2    0.5
> probe2        0.4    0.9    0.7
> probe3        0.6    0.7    0.4
>
>
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