R help - Nov 2008 - HELP ON SCALING GENE EXPRESSION DATA TO -1,0,1

Hello R-Community,

I am a rookie in R and I am fascinated with the power of bio computing
by R. I am analysing gene expression data from Real time PCR. I have
used absolute gene quantitation to measure gene copy number in all my
transcripts. All my data has been normalised them to a housekeeping
gene, which is constitutive expressed.

My problem is as follows.
After normalising some of the genes (which are feature vectors in my
matrix of 26 treatment conditions) are up regulated to over 50 fold.
Now, when plot my heatmap.2 of the matrix, almost everything shows up
as red, in a green-red colour scale.
 i.e. from -1,0,1. Is there a  way to scale all the data on the matrix
such that when i plot it on a heat map it it reflecting the relative
expression of of each feature, against the treatment condition without
being fixed to the -1, to 1 scale.
Below is how the code i used.

library(gplots)
zcz<- read.table("chitekete.csv", header = T, row.names=1,
sep=",");
xcc <- cor(zcz);
pdf("SIGA.pdf", height=10,width=9)
heatmap.2(xcc, margins= c(9,9), col = bluered(64), trace=c("none"),
breaks=c(seq(-1,1,1/32)), symkey=TRUE, density.info="histogram",
cexRow=1)

I thank you all.

Paul



-- 
BEST

Paul Murima

"paul murima" <paul.murima at gmail.com> writes:
> Hello R-Community,
>
> I am a rookie in R and I am fascinated with the power of bio computing
> by R. I am analysing gene expression data from Real time PCR. I have
> used absolute gene quantitation to measure gene copy number in all my
> transcripts. All my data has been normalised them to a housekeeping
> gene, which is constitutive expressed.
>
> My problem is as follows.
> After normalising some of the genes (which are feature vectors in my
> matrix of 26 treatment conditions) are up regulated to over 50 fold.
Do you know about http://bioconductor.org ? Reviewing their mailing
list archives and asking on their mailing list will likely lead to a
number of informed opinions about normalization.

Martin
> Now, when plot my heatmap.2 of the matrix, almost everything shows up
> as red, in a green-red colour scale.
>  i.e. from -1,0,1. Is there a  way to scale all the data on the matrix
> such that when i plot it on a heat map it it reflecting the relative
> expression of of each feature, against the treatment condition without
> being fixed to the -1, to 1 scale.
> Below is how the code i used.
>
> library(gplots)
> zcz<- read.table("chitekete.csv", header = T, row.names=1,
sep=",");
> xcc <- cor(zcz);
> pdf("SIGA.pdf", height=10,width=9)
> heatmap.2(xcc, margins= c(9,9), col = bluered(64),
trace=c("none"),
> breaks=c(seq(-1,1,1/32)), symkey=TRUE, density.info="histogram",
> cexRow=1)
>
> I thank you all.
>
> Paul
>
>
>
> -- 
> BEST
>
> Paul Murima
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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