Microarray Profile/Trend Plots (Z-score Plots)

Question

[pixie@bioinfo]

I have a gene expression profile matrix corresponding to a gene cluster. I want to plot a microaaray profile plot to see whether all the genes are varying in the same way. How do I go about it in R or MATLAB ?

here is an example of the plot, Y-axis has the z-scores and x-axis has the samples.

http://rice.plantbiology.msu.edu/cgi-bin/generate_trend_plot_page.pl?experiment=E-MEXP-1766&module=turquoise&gene_feat_name=LOC_Os02g04780

Here is the link to the paper where these plots have been used.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022196

Thanks

[Madelaine Gogol]

Maybe put an example of what your data looks like.

Answer 1

[David Quigley]

I don't think I understand your question perfectly, but if you mean, "how can I plot a hierarchical cluster of microarray data, when the data are represented as a matrix with genes/probes in rows and samples in columns", an answer in R would be:

plot(hclust(dist(M)))

dist() calculates the distance between rows; there are a variety of metrics for distance. hclust() creates an object from a distance matrix which is then used by plot() to generate a picture. To learn more:

?dist
?hclust

There are also functions which will plot the gene expression values as a heatmap. To get started, type

?heatmap

[pixie@bioinfo]

Hi, I have given an example for the kind of the plot I am looking for. Thanks