## aCGH / Plot copy-number-induced gene expression

### Description

Plot the expression level of specified gene(s) for a copy number vs. expression comparison. This tool must be run on the output from the tool "Test for copy number induced expression changes" - cn-induced-expression.tsv.

### Parameters

- Gene IDs of the genes to be plotted (...) [1]
- Gene symbols of the genes to be plotted (...) [empty]
- Image width (200...3200) [600]
- Image height (200...3200) [600]

### Details

For each gene, the samples are divided into two groups either "loss vs. no-loss (normals and gains)" or "no-gain (losses and normals) vs. gain" depending on the amount of gains and losses for that particular gene. The expression values of the specified gene(s) are then plotted across the two groups. Each sample is plotted as an open blue circle, and the center of the circle marks the expression level of the particular gene in that sample. The radius of the circle is proportional to the corresponding copy number call probability (e.g. a large circle in the "loss" group means that for this particular sample, a call for loss was made with high probability). Call probabilities equal to zero reduce circles to dots. The red filled circles have a radius proportional to the estimated expected call probabilities, with their centerpoints at the estimated mean expression for the respective call.

### Output

An image showing the expression levels for the gene(s) of interest in the two groups defined by copy number.

### References

Wieringen et al. (2009) Nonparametric testing for DNA copy number induced differential mRNA gene expression. Biometrics 65: 19-29