X. laevis

One of our users asked for the files necessary to run ExpressionPlot on Affymetrix Xenopus laevis arrays:

Xenopus laevis

I was surprised to learn that there is no X. laevis genome yet. I took Affymetrix’s netaffx data file and probe tables and created some ExpressionPlot-compatible files by pretending each consensus sequence (basically Affymetrix’s idea of a transcript) was a chromosome. You can get the files using util/EP-manage.pl:

util/EP-manage.pl get_array X_laevis_2
util/EP-manage.pl get_annot Xl2

The name “Xl2” for the annotation might be a little confusing since most of the other annotations are named after genome assemblies—here it really refers to being based on affymetrix’s X_laevis_2 consensus sequences.

If anyone needs the files for other arrays please don’t be shy to put in the request—someone else may also find it useful! Also, if you have any problems with these files please be sure to contact the ExpressionPlot discussion group so we can help you or fix the problems.

Leave a Reply

You must be logged in to post a comment.

A web-based framework for analysis of RNA-Seq and microarray gene expression data