README-Probes2Names Created January 24, 2005 by John Newman (newmanj@u.washington.edu) This document describes the use of Probes2Names, a collection of Perl programs for converting microarray probe IDs to HUGO gene symbols. Probes2Names requires a computer with Perl5 and a UNIX-like command shell. Probes2Names is released under the GNU General Public License (see the file "LICENSE"), with the following notice: -------------------- Copyright (C) 2005 John C. Newman This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. -------------------- -------------------- Contents: -------------------- I. Translator libraries II. p2n.pl III. add_at.pl -------------------- I. Translator libraries -------------------- p2n.pl and add_at.pl are Perl application that will help convert a list of microarray probe identifiers to the HUGO gene symbols of the genes they each represent. They require a "translator library" file for the microarray platform in question. These are tab-delimited text files in the format "ProbeIDGeneSymbol", with each entry on a new line. Only probes that represent named genes need be included. The files are identical to the translator libraries used by L2L. Probes2Names comes with a variety of translator files for Affymetrix, Aglient, and NIH/NIA cDNA microarrays. Translator library files must be in the "library" subdirectory, in the same directory as the applications. -------------------- II. p2n.pl -------------------- p2n.pl takes three arguments at the command-line: library file, input file, and output file. The library file must the file name of the appropriate translator library in the "library" subdirectory (e.g. u133set). The input file can be named anything, but must contain a list of probe IDs, one per line. The output file is just the location/name of the file you wish the output to be written to. A typical use of p2n.pl might therefore look like this: ./p2n.pl u133a someinput myoutput The program will also report its progress to the terminal, including any probes it cannot find matches for in the translator library. -------------------- III. add_at.pl -------------------- Occasionally, published lists of Affymetrix probe IDs truncate the IDs by removing the suffixes: "_at", "_s_at" or "_x_at". add_at.pl will add the correct suffix on to a list of such truncated Affymetrix probe IDs. Like p2n.pl, add_at.pl takes three arguments at the command-line: library file, input file, and output file. The library file must the file name of the appropriate translator library in the "library" subdirectory (e.g. u133set). The input file can be named anything, but must contain a list of probe IDs, one per line. The output file is just the location/name of the file you wish the output to be written to. A typical use of add_at.pl might therefore look like this: ./add_at.pl u133a someinput myoutput The program will also report its progress to the terminal, including any probes it cannot find matches for in the translator library. Since the output file contains a list of now-complete Affymetrix probe IDs, it can used directly as the input file for p2n.pl. -------------------- END OF README FILE --------------------