Hello, Using getGEO, I got "GSE8500_series_matrix.txt.gz" and saved it at a folder. I would like to extract all 43 .cel files and start analyzing them using bioconductor. Please let me know what are the next steps. Thanks, Jerry [[alternative HTML version deleted]]

Hi, Jerry. There are no .cel files associated with GSE8500 (they were not submitted to NCBI GEO). If you want access to those files, your only option is to contact the authors of the original paper. Assuming that you are comfortable with working with the data as deposited at NCBI GEO, your task is very simple: library(GEOquery) eset = getGEO('GSE8500')[[1]] The eset variable is an ExpressionSet object, which is the standard container for gene expression data in R. There is no need to parse the .txt.gz file separately, as GEOquery has already done that. You can get help by typing ?ExpressionSet for details on your eset object. If you need more guidance from there, it will help if you can expand on what you mean by "start analyzing them using bioconductor". Sean On Thu, Feb 13, 2014 at 2:27 PM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Hello, > > > Using getGEO, I got "GSE8500_series_matrix.txt.gz" and saved it at a > folder. > I would like to extract all 43 .cel files and start analyzing them using > bioconductor. Please let me know what are the next steps. > > Thanks, > > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]