Hi, I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the RLMM package. This is an non-supported tool by Affy and therefore I hope someone else can help me out. Affymetrix provides the (platform independent) C++ source code at http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and says "This is the source code for the gtype_to_cel_pq tool. To build this application you will also need to download and compile the File SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source code provided has only been compiled and tested on a Linux system using the g++ version 3.3 compiler.". Has anyone successfully built this tool on Unix, Linux or even Windows (Cygwin?) and if so could you please tell me what compile and link options you used for g++? I am aware of Nusrat Rabbee's pre-compile Linux version at www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html but it does not run on the Unix system I have access. Best wishes Henrik Bengtsson

Hi Henrik, Apparently the Makefile didn't make it to the tarball we posted - that was a mistake. We'll repost, in the meantime find it included below. It has been compiled and tested on linux (on both i386 & amd64 processors). Should work on other platforms too, though we haven't tested. -S ------------------BEGIN MAKEFILE---------------------- # # This code requires the Affymetrix FileSDK to compile - it is available from # <http: www.affymetrix.com="" support="" developer="" filesdk="" index.affx=""> # # There are several constants that may need to be defined to enable compilation # and execution on specific operating systems. These are : # # Makefile variables you MUST set: # SDK_FILE Set to wherever the FileSDK is located. # SDK_PORTABILITY Set to wherever the FileSDK is located. # # Compilation variables which you may need to add to the CPPFLAGS variable below: # IS_BIG_ENDIAN Define if the machine represents data in big endian format. # _INCLUDE_UNISTD_HEADER_ Define if the UNISTD.H header file is used by your C++ compiler. # WIN32 Define if using the MSVC++.NET compiler. # _USE_MEM_MAPPING_ Define if you want to enable memory mapping for BAR, BPMAP, CDF and CEL file reading. # SDK_PORTABILITY:=../../../portability SDK_FILE:=../../../file CPPFLAGS = -O2 -I $(SDK_FILE) -I $(SDK_PORTABILITY) # The following line is an example of what you should use on a big endian machine #CPPFLAGS = -O2 -I $(SDK_FILE) -I $(SDK_PORTABILITY) -DIS_BIG_ENDIAN CC=g++ SOURCES=\ $(SDK_FILE)/CELFileData.cpp \ $(SDK_FILE)/CDFFileData.cpp \ $(SDK_FILE)/FileIO.cpp \ hash.cpp \ gtype_cel_to_pq.cpp OBJECTS=$(SOURCES:.cpp=.o) EXE=gtype_cel_to_pq all: $(EXE) $(EXE): $(OBJECTS) $(CC) $(CPPFLAGS) $(OBJECTS) -o $@ clean: -rm -rf $(OBJECTS) $(EXE) ------------------END MAKEFILE---------------------- On Tue, 18 Oct 2005, Henrik Bengtsson wrote: > Date: Tue, 18 Oct 2005 19:25:16 +1000 > From: Henrik Bengtsson <hb at="" maths.lth.se=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Affymetrix gtype_cel_to_pq > > Hi, > > I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the > RLMM package. This is an non-supported tool by Affy and therefore I > hope someone else can help me out. > > Affymetrix provides the (platform independent) C++ source code at > http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and > says "This is the source code for the gtype_to_cel_pq tool. To build > this application you will also need to download and compile the File > SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source > code provided has only been compiled and tested on a Linux system > using the g++ version 3.3 compiler.". > > Has anyone successfully built this tool on Unix, Linux or even Windows > (Cygwin?) and if so could you please tell me what compile and link > options you used for g++? > > I am aware of Nusrat Rabbee's pre-compile Linux version at > www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html but it does not > run on the Unix system I have access. > > Best wishes > > Henrik Bengtsson > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Basically the Fusion SDK (which is the File SDK mentioned below) is implemented through the affxparser package. It works on Mac OS, Linux'es but currently not on Solaris and Windows. The problem seems to be tied to low-level differences in the standard libraries. We are working with the people from affy to resolve these issues. But as I said, if Linux/MacOS is ok for you, you are good to go. Kasper On Oct 18, 2005, at 2:25 AM, Henrik Bengtsson wrote: > Hi, > > I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the > RLMM package. This is an non-supported tool by Affy and therefore I > hope someone else can help me out. > > Affymetrix provides the (platform independent) C++ source code at > http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and > says "This is the source code for the gtype_to_cel_pq tool. To build > this application you will also need to download and compile the File > SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source > code provided has only been compiled and tested on a Linux system > using the g++ version 3.3 compiler.". > > Has anyone successfully built this tool on Unix, Linux or even Windows > (Cygwin?) and if so could you please tell me what compile and link > options you used for g++? > > I am aware of Nusrat Rabbee's pre-compile Linux version at > www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html but it does not > run on the Unix system I have access. > > Best wishes > > Henrik Bengtsson > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Oh yeah, if you are interested in Unixes and Cygwin in relation to the Fusion SDK, you will probably not get it to work on Solaris with GCC less than 3.4 and probably not on Cygwin either. The problem here is that the SDK supplies multi-byte character support through (the standard) class wstring which is not supported for Gcc on Solaris before version 3.4 and which was not supported on Cygwin last time I had a look (some months ago). Kasper On Oct 18, 2005, at 2:25 AM, Henrik Bengtsson wrote: > Hi, > > I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the > RLMM package. This is an non-supported tool by Affy and therefore I > hope someone else can help me out. > > Affymetrix provides the (platform independent) C++ source code at > http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and > says "This is the source code for the gtype_to_cel_pq tool. To build > this application you will also need to download and compile the File > SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source > code provided has only been compiled and tested on a Linux system > using the g++ version 3.3 compiler.". > > Has anyone successfully built this tool on Unix, Linux or even Windows > (Cygwin?) and if so could you please tell me what compile and link > options you used for g++? > > I am aware of Nusrat Rabbee's pre-compile Linux version at > www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html but it does not > run on the Unix system I have access. > > Best wishes > > Henrik Bengtsson > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >