Question: Microarray Profile/Trend Plots (Z-score Plots)
gravatar for pixie@bioinfo
6.7 years ago by
pixie@bioinfo1.4k wrote:

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.

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


microarray matlab R • 2.7k views
ADD COMMENTlink modified 6.1 years ago • written 6.7 years ago by pixie@bioinfo1.4k

Maybe put an example of what your data looks like.

ADD REPLYlink written 6.7 years ago by Madelaine Gogol5.1k
gravatar for David Quigley
6.7 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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:


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:


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

ADD COMMENTlink written 6.7 years ago by David Quigley11k

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

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by pixie@bioinfo1.4k
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