Hi everyone I have been searching for a package/module to analyse Agilent miRNA with Bioconductor. I google it but couldn't find any indication of a package or a workflow with modules available on the Bioconductor website. I have seen that marray opens Agilent data, but it fails when the data if from a miRNA experiment. I also tried Agi4x44PreProcess and it also fails to open the data. Any pointers, ideas or suggestions are more than welcomed. Thanks in advance Paulo

Hi Paulo, I had the same problem. I solved it by modifie the read.AgilentFE function (Agi4x44ProProcess) by removing the stop point for "Sequence and chr_coord" and additionally set "dd$genes=ddaux$genes[,c(4:8)]". This way at least the data reading works and one can use the normalization step(vsn). Mapping won't work due to the missing map-db and the filtering is still making Problems. But this can be solved by manualy filter the results. The RGlist contains all needed Flags. Hope this was helpful. Marten > Hi everyone > > I have been searching for a package/module to analyse Agilent miRNA > with Bioconductor. I google it but couldn't find any indication of a > package or a workflow with modules available on the Bioconductor > website. I have seen that marray opens Agilent data, but it fails when > the data if from a miRNA experiment. I also tried Agi4x44PreProcess > and it also fails to open the data. > > Any pointers, ideas or suggestions are more than welcomed. > > Thanks in advance > > Paulo > > _______________________________________________ > 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 >