Hi Galaxy Users,
I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu)
After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong?
In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening.
Cheers, Ivan
P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff..