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

[Roebuck,Paul L]

On 8/23/12 7:37 AM, "David Lyon" <david_lyon3 at yahoo.com> wrote:

> 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 ³control genes²) 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

SuperCurve* has a normalization function that normalizes
by median, variable slope, and housekeeping genes.
But it's geared towards slightly larger problems...
It's used in production by our Core Labs to process their RPPAs.

<http://bioinformatics.mdanderson.org/main/SuperCurve:Overview>

* Shameless plug