Please help....normalization by the median of some control genes

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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