The most recent change was from binary XDA format to binary COMMAND CONSOLE (aka CALVIN) format. In any case affyio (which is giving the back end of things like affy's ReadAffy()) supports reading this format, and interchangably mixing it with the previous formats. The tools in affxparser are presumably also able to do the same (since it's built around affymetrix own file sdk). Ben > Hi Iain, > > IAIN GALLAGHER wrote: >> Hello list. >> >> This is not technically a bioconductor problem but... I have been >> informed that during the last year or so Affymetrix have changed the >> way they make / generate .CEL files. I was wondering whether this is >> likely to affect the results one would obtain running an analysis >> from .CEL files onwards. > > If you mean the change from ASCII to binary format, this happened a few > years ago. There are some facilities to change between the formats, but > this should be unnecessary, as most tools that you are likely to use > will use either format without complaint. > > Best, > > Jim > > >> >> Thanks >> >> Iain >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ Bioconductor mailing >> list Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >> archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

On Fri, Jun 20, 2008 at 8:06 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Iain, > > IAIN GALLAGHER wrote: >> >> Hello list. >> >> This is not technically a bioconductor problem but... I have been >> informed that during the last year or so Affymetrix have changed the >> way they make / generate .CEL files. I was wondering whether this is >> likely to affect the results one would obtain running an analysis >> from .CEL files onwards. > > If you mean the change from ASCII to binary format, this happened a few > years ago. There are some facilities to change between the formats, but this > should be unnecessary, as most tools that you are likely to use will use > either format without complaint. Affymetrix has introduced a more generic binary file format (think XML but an inhouse format) that applies to several of their file formats, e.g. CEL and CDF. That might be what you are thinking of. The affxparser package handles those files automatically because it utilizes Affymetrix' Fusion SDK library to read the files. So, any package reading files using affxparser can deal with those as well. Cheers Henrik > > Best, > > Jim > > >> >> Thanks >> >> Iain >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ Bioconductor mailing >> list Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >> archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >