hi derek, I have a 400mHz G4, with X 10.2.5 and am using Jan de Leeuw's precompiled R package at http://gifi.stat.ucla.edu/pub/. All you would need is the MacOsX developer tools and X11 from apple, you could also install fink if you want. I was getting errors like yours(with 1.6.2) and I recall it had to do with the cdf file not being installed, it is available from the bioconductor website and can be installed from your root directory using : sudo R CMD INSTALL "path to the cdf file". I am new to the list and I have also seen the error messages when trying to read in cel files, and when using normalize.loess as described in paul boutros email. I did install the affy developer package, along with the devel packages of tkWidgets and Biobase, everything seems to be fine for now, except that the loess normalization gives a memory error for the size of the matrix?: Done with 1 vs 2 in iteration 1 Done with 1 vs 3 in iteration 1 Done with 2 vs 3 in iteration 1 1 0.001657622 Warning messages: 1: k-d tree limited by memory. ncmax= 5002 2: k-d tree limited by memory. ncmax= 5002 3: k-d tree limited by memory. ncmax= 5002 Does anyone have suggestions on how to increase the size of ncmax? Best, mike > > Message: 5 > Date: Mon, 28 Apr 2003 14:00:37 -0700 > From: "Stirewalt, Derek L" <dstirewa@fhcrc.org> > Subject: [BioC] MAC INSTALLATION AFFY PACKAGE > To: "'bioconductor@stat.math.ethz.ch'" > <bioconductor@stat.math.ethz.ch> > Message-ID: <b1c5649a402dd51190930002b330a181014388af@shemp.fhcrc.org> > Content-Type: text/plain; charset="iso-8859-1" > > HI, > WE ARE TRYING TO INSTALL AFFY PACKAGE AND BIOC ON A IMAC WITH OS10 AND > WHEN > WE TRY TO READ A CEL FILE HERE IS WHAT WE GET: > > >> library(affy) > Welcome to Bioconductor > To view some introductory material -- look at our vignettes > Simply type: openVignette() > to see the available vignettes > To read a vignette see the openVignette help page for details > Creating a new generic function for "summary" in package > Biobase > > Attaching package `Biobase': > > > The following object(s) are masked from package:base : > > split summary > > > Attaching package `affy': > > > The following object(s) are masked from package:base : > > barplot boxplot colnames hist history image ncol nrow > >> Data <- ReadAffy() > Error in getInfoInAffyFile(filename, "CEL", "HEADER", "DatHeader", > compress = > compress) : > Cannot open the file Wilson:Applications:rm162::0126192.CEL. > SO IT SEEMS THAT BIOC IS ABLE TO GET AFFY WORKING BUT READNG THE CEL > FILE > SEEMS T BE A TROUBLE. WE ARE RUNNING BIOC on R1.6.2 and the Affy > package is > the routine one, not the developmental package. > ANY HELP WELCOME ! THANKS > > Derek L. Stirewalt, MD > Associate in Clinical Research > D4-100, FHCRC > 1100 Fairview Ave N > Seattle, WA 98109 > (206)-667-5113 > -------------------------------------------------- Michael J. McDonald Ph.D. Univesite of Geneve c/o Duboule Lab Department of Zoologie and Biologie Animale Quai Ernest-Ansermet 30 CH-1211 Geneve 4 phone 41.22.702.67.94