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RE: magetab2magerdf

From: Michael Miller <mmiller@teranode.com>
Date: Wed, 6 Jan 2010 12:55:16 -0500
Message-ID: <6401DB16544A5B4AA279B921F43547EC0675292E@MI8NYCMAIL16.Mi8.com>
To: "Jim McCusker" <james.mccusker@yale.edu>
Cc: "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
hi jim,

 

i see the problem now, i went to ArrayExpress.  the one at the google
site was set up for demonstration purposes at MGED12 and it doesn't
match the ArrayExpress version, which is the official one.  i helped in
that demo and none of us caught that.  if you follow the link in the
google version to the actual raw file at the ftp site, it references the
'1d1S15.txt.txt' style names.

 

so that is good news, i would recommend regenerating with the
ArrayExpress version of all the files.

 

cheers,

michael

 

From: Jim McCusker [mailto:james.mccusker@yale.edu] 
Sent: Wednesday, January 06, 2010 9:37 AM
To: Michael Miller
Cc: w3c semweb HCLS
Subject: Re: magetab2magerdf

 

On Wed, Jan 6, 2010 at 12:18 PM, Michael Miller <mmiller@teranode.com>
wrote:

"Unless I have a bug, ..."

pretty sure you do, especially since there is no 'Array Data Matrix
File' column in the SDRF plus none of the raw data file names in the
ArrayExpress zip file appear to be referenced in the RDF (or at least
the one i checked) and the referenced raw file in the RDF doesn't exist
in Array Express for that experiment.

 
A closer look at the SDRF reveals these columns:

Array Data Matrix File
E-MEXP-986-raw-data-1321832728.txt
E-MEXP-986-raw-data-1321832722.txt
E-MEXP-986-raw-data-1321832716.txt
E-MEXP-986-raw-data-1321832734.txt

and

Derived Array Data Matrix File
E-MEXP-986-processed-data-1343528010.txt
E-MEXP-986-processed-data-1343528012.txt
E-MEXP-986-processed-data-1343528010.txt
E-MEXP-986-processed-data-1343528012.txt


I used
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-M
EXP-986/E-MEXP-986.sdrf.txt as the SDRF for that accession. Am I missing
something?

Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Wednesday, 6 January 2010 17:55:47 UTC

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