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
Please help....normalization by the median of some control genes
4 messages · David Lyon, Rui Barradas, arun +1 more
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