Hi Jim, Thanks for your reply and insight. I will check out your suggestions, and evaluate to best strategy for generating the expression data set and then analysing it 'externally'. Best, Dan James W. MacDonald wrote: > Hi Dan, > > Dan Strumpf wrote: >> Hello, >> >> I am new to exon array analysis and have used the >> huex10stv2cdf_1.15.0.tar.gz package (downloaded from >> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz >> )as a cdf source/mapping for processing Human exon array data within >> 'affy' package. Processing went smoothly without any error messages. >> Noticed some communication about this package in Oct. 2007, and am not >> clear if results using it are relaible. > > I don't know anything about that cdf, but if it is similar to the > modified cdf that you can get from PICR for exonmap, you should get > pretty much the same values, as exonmap uses the affy package and a > modified cdf to compute expression values. > > The upside to using exonmap is that you have ways to map the probesets > to their location on the genome, and could thereby filter out those that > hit what are considered to be inter-genic or intronic positions. > > I don't know if you will be able to use gcrma, as there are no MM probes > on the exon chips. Instead they just have two sets of probes that are > designed to measure background. > > >> I am interested in processing Human exon array data also with gcRMA >> and am wondering if should use the above package or use >> xps/exonmap/oligo instead? Would like to know also what are to options >> for differential expression analysis equivalent to samr limma or >> RankProd for paired samples from within exon array analysis packages >> or could the preprocessed/normalized data be exported and used with >> xps/exonmap/oligo packages. > > Pre-processing and differential expression are in general handled by > different packages. For instance, you don't use the affy or gcrma > package to look for differentially expressed genes, and the same holds > true for xps, exonmap, and oligo. > > That said, there isn't really that much different between the exon chip > data and the 3' biased arrays, so tools like limma and RankProd should > be fine for analyzing these data. > > Best, > > Jim > > >> >> Thanks, >> >> Dan >> >> _______________________________________________ >> 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 >