can you tell me what version of the affy package you are using (on 1.8.1)? help(package=affy) the latest version (release) 1.3.28 supports binary files. Thanks, Ben On Sun, 2004-02-29 at 14:41, Isaac Mehl wrote: > recently tried to use ReadAffy fucntion for some CEL files and received: > > > Data <- ReadAffy() > Error in read.affybatch(filenames = filenames, phenoData = phenoData, : > The file /cool/delta_microarray/YZ04022501.CEL does not look > like a CEL file > > most likely because the CEL file is binary. found an old thread for > bioconductor which said the newest affy devel package can handle binary > files and runs in R 1.8.1. however when i try: > > > getBioC(libName="affy", relLevel="devel") > Running getBioC version 1.2.52.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to > bioconductor@stat.math.ethz.ch. > > Error in getBioC(libName = "affy", relLevel = "devel") : > > You are currently running R version 1.8.1, however R version 1.9.0 is > required. > > am i doing something wrong here?? For anyone else having this problem i > found a work around. go to: > http://www.affymetrix.com/support/developer/tools/affytools.affx > there is a program here that will convert binary to ASCII and vise versa > on a windows machine. > > -isaac > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad

On Sun, 2004-02-29 at 16:15, Isaac Mehl wrote: > ben, > > thank you for the reply. i am using affy 1.4.1. in the email thread > you mentioned 1.4.4 can handle binary files. > > -isaac > Yes, what happened is that around 1.4.4 binary cel file compatibility was introduced into the development series. The official release version at this time was 1.3.26 and did not have the ability to read binary cel files. At about version 1.4.6 the development version started to require R-1.9 (in development). So binary cel file compatibility was ported back to the release tree as affy version 1.3.28. In summary Can read binary cel files Release 1.3.27 Development 1.4.4 and newer (After 1.4.6 required R-1.9.X) Cannot read binary cel files Release 1.3.26 and earlier Development 1.4.0-1.4.3 Hope this clarifies the issue. Ben