# [BioC] matching expression profiles

Thomas Girke thomas.girke at ucr.edu
Tue Jan 15 23:54:25 CET 2008

```For this, you could correlate the expression profile of your gene of interest against
all the others on your chip and then plot the profiles in form of a line graph.

Here is a short example using some random data:

## (1) Correlation Search
x <- data.frame(y1=rnorm(10),y2=rnorm(10),y3=rnorm(10),y4=rnorm(10))
rownames(x) <- month.name[1:10]
# correlation analysis gene "August" against all others
y <- data.frame(apply(as.matrix(x), 1, cor, as.vector(as.matrix(x["August",])), method="pearson"))
names(y)[1] <- c("PearsonCC")
# Combine data and sort by correlation coefficient
y <- cbind(x, y)
y[order(-y[,5]), ]

## (2) Plot Top Five Hits in Form of a Line Graph

y <- t(y[1:5,1:4])
plot(y[,1], type="l", lwd=2, col="blue") # Plots a line graph
split.screen(c(1,1))
plot(y[,1], ylim=c(0,1), xlab="Measurement", ylab="Intensity", type="l", lwd=2, col=1)
for(i in 2:length(y[1,])) {
screen(1, new=FALSE)
plot(y[,i], type="l", lwd=2, col=i, xaxt="n", yaxt="n", ylab="", xlab="", main="", bty="n")
}
close.screen(all=TRUE) # Pl

On Mon 01/14/08 09:33, Lana Schaffer wrote:
> Jim,
> I am just asking about the expression of a single gene across all the
> samples.
> I have been reminded that genefinder would be a for me and I have used
> it before.
> Thanks,
> Lana
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Monday, January 14, 2008 9:25 AM
> To: Lana Schaffer
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] matching expression profiles
>
> Hi Lana,
>
> What exactly do you mean by 'expression profiles'?
>
> If you mean e.g., person A says these 100 genes are interesting in the
> experimental system I am investigating, and I want to compare my results
> to hers, then I think you want to use GSEA.
>
> I am most familiar with the variant in the Category package, but you
> might also consider PGSEA or GSEAbase, depending on where your
> expression profile comes from.
>
> Best,
>
> Jim
>
>
>
> Lana Schaffer wrote:
> > Friends,
> > What packages would you recommend in Bioconductor that would match
> > expression profiles similar to a given expression profile and perhaps
> > draw them ?
> > Thanks,
> > Lana Schaffer
> >
> > 	[[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
> _______________________________________________
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>

--
Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437

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