Plotting Mas5Calls

Question

[Assa Yeroslaviz]

Hi,

we have a set of arrays from the mouse genome. We ran the present-absent-call on them to see which of the probes are present and/or absent. The reason for that is not important for the question.

What we are looking for now is a good way to plot this data.

We have 12 arrays from four different conditions. these can be however separated into two groups.

I would like to ask you guys, if you knows of a good way to plot present-absent values.

The answers searched with these plots will be

• how many genes are present in each of the array(groups)?

• What genes are common to each of the array(-groups) in their absence or presence?

I would appreciate your help.

Thanks

Answer 1

[Sean Davis]

For the first question, I'd suggest a barplot for the array-level data and a boxplot or dotplot for the array groups. For the second, you might try a simple heatmap.

As an aside, if this analysis is being conducted to give you biological insight and not just simple QA/QC, you should look at this paper:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013751&tool=pmcentrez&rendertype=abstract

and consider using these methods rather than simple present/absent calls.

[Assa Yeroslaviz]

thanks for the response. But as I am working here with drosophila arrays, I don't see how to do it with this barcode project. Apparently they have only mouse and human arrays. Where can I find the methods part of the paper? or of the project?

[Sean Davis]

If you are interested, contact Matt McCall and he may be able to develop something for drosophila. The original methods are described here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154617/