Hello list, I am working on illumine bead array expression data. The data was output from GenomeStudio with probe annotation. There is a column called PROBE_TYPE, with three values: A, I and S. What do these values mean, antisense, intron and sense? Antisense and sense are string relative to the target gene, not to the reference genome, right? Why intron and antisense probes are needed? I couldn?t find the description info on Internet. Thanks a lot! Heyi

Hi Heyi, The PROBE_TYPE value doesn't refer to the strand. ?It represents the isoform specificity of the probe i.e. does it target all known isoforms, only one isoform or is there only one known isoform. ?The assignments are as follows: A?- probe targets all isoforms I?- probe targets only one of multiple isoforms S?- probe targets the only isoform On 27 June 2012 18:36, heyi xiao <xiaoheyiyh at="" yahoo.com=""> wrote: > > Hello list, > I am working on illumine bead array expression data. The data was output from GenomeStudio with probe annotation. There is a column called PROBE_TYPE, with three values: A, I and S. What do these values mean, antisense, intron and sense? Antisense and sense are string relative to the target gene, not to the reference genome, right? Why intron and antisense probes are needed? I couldn?t find the description info on Internet. Thanks a lot! > Heyi > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Mike Smith PhD Student Computational Biology Group Cambridge University