Dear Eric, thank you for your answer.
Your workaround works for the pheno file.

A related question is: the affybatch and the
eset file formats require to upload two files
(rispectively the pheno and the eset/affybatch).

Is it normal to have finally only
the pheno one in the History?

I.

Hi Ivan,

I can provide an explanation about the first part at least.  You are seeing that 
"##failed" message due to a bug in Galaxy core code that I've previously raised on this 
list.  The path you see there is where the .pheno file should (and does) end up after the tool is 
done.  However, the code that generates the "##failed" message is getting called before 
the .pheno file has been moved to that path from its temporary location.  Hence, it can't be found 
there at that point in execution time.

While requiring a workaround is not ideal, a very simple one does exist.  In the history item for 
your uploaded dataset, click on the pencil ("Edit attributes") and then click the button 
that says "Auto-detect".

Best,
Eric

________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Ivan Merelli [ivan.mere...@itb.cnr.it]
Sent: Wednesday, November 09, 2011 7:12 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] microarray&  NGS

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..

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