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
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written
by
Assa Yeroslaviz
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.
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?
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/
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