Hi there I am trying to use gcrma to normalise a human gene st array data set. I read the following message from Feb 2010 that said that gcrma had not yet been implemented for the gene st arrays: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 7023/match=gcrma+hugene Is this still the case? If not, and gcrma is implemented for the human gene st array, can anyone explain why I get the following error after running this code: library(gcrma) library(hugene10stv1cdf) Data <- ReadAffy(celfile.path='~/Andrew/Tim_Woods/cel_files',cdfname='hugene10 stv1cdf') ai <- compute.affinities(cdfName(Data)) *Error in get(probepackagename) : object 'hugene10stv1cdfprobe' not found* Regards Andrew [[alternative HTML version deleted]]

I am afraid this has not been done yet. At first we were waiting for oligo to stablize how it parses the data first, but after it did I have not had time to get to it. On 9/13/2010 10:10 AM, Andrew Einhorn wrote: > Hi there > > I am trying to use gcrma to normalise a human gene st array data set. I > read the following message from Feb 2010 that said that gcrma had not yet > been implemented for the gene st arrays: > http://article.gmane.org/gmane.science.biology.informatics.conductor /27023/match=gcrma+hugene > > Is this still the case? If not, and gcrma is implemented for the human gene > st array, can anyone explain why I get the following error after running > this code: > > library(gcrma) > library(hugene10stv1cdf) > Data<- > ReadAffy(celfile.path='~/Andrew/Tim_Woods/cel_files',cdfname='hugene 10stv1cdf') > ai<- compute.affinities(cdfName(Data)) > > *Error in get(probepackagename) : object 'hugene10stv1cdfprobe' not found* > > Regards > > Andrew > > [[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 -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu