R help - Aug 2012 - Please help....normalization by the median of some control genes

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

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
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

HI,

You could try:
limma package: normalizeWithinArrays()
A.K.



----- Original Message -----
From: David Lyon <david_lyon3 at yahoo.com>
To: "r-help at r-project.org" <r-help at r-project.org>
Cc: 
Sent: Thursday, August 23, 2012 8:37 AM
Subject: [R] Please help....normalization by the median of some control genes

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


______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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 ?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

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