Dear all, I'm a beginner in the preprocessing of microarray data. Currently, I'm facing the extraction of the expression data matrix from the raw data of an antibody microarray. I have GPR files from two different arrays before and after the washing, and a GAL file. How can I do that? I have PANORAMA arrays (SIGMA), so anyone knows how can I do the normalization of the expression data? Any ideas on these issues will be very welcome. Regards, Núria [[alternative HTML version deleted]]

Dear N?ria many aspects of what you will be doing will be similar to transcription microarrays, and the limma package is a mature and well-documented place to get started. There will probably be specific questions re normalisation and quality assessment for your array. The respective chapters in the Bioc books [1-2] can give you some ideas, in addition you might benefit from teaming up with a local statistician or bioinformatician. Best wishes Wolfgang [1] http://www.bioconductor.org/help/publications/books/bioinformatics- and-computational-biology-solutions [2] http://www.bioconductor.org/help/publications/books/bioconductor-case- studies Il Feb/2/11 5:18 PM, nqueralt at clinic.ub.es ha scritto: > Dear all, > > > > I'm a beginner in the preprocessing of microarray data. Currently, I'm facing the extraction of the expression data matrix from the raw data of an antibody microarray. I have GPR files from two different arrays before and after the washing, and a GAL file. How can I do that? > > > > I have PANORAMA arrays (SIGMA), so anyone knows how can I do the normalization of the expression data? > > > > Any ideas on these issues will be very welcome. > > > > Regards, > > > > N?ria > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber