Hi, I have previously used R to analyse HG-U133A and B arrays and everything was perfect. I like very much how I could see the PCA plots... However, a colleague of mine has started using arrays "human gene 1.0 st" and we found a problem when we wanted to analyse them. Dr Irizarry told me that this array is not supported in the affy package, and that he thinks oligo package does. But he suggested me to ask in this e-mail. Thank you very much for your help. Waiting for your answer, Best regards, Amets Sáenz Dra. Amets Sáenz Unidad Experimental Hospital Donostia Pº Dr Begiristain s/n San Sebastián 20.014 Tel: 943 00 70 61 FAX: 943 00 70 61 [[alternative HTML version deleted]]

Hi Amets. You have a few options for Gene 1.0 ST arrays in and outside of R. Check out the following thread from earlier this year. It captures several options: http://thread.gmane.org/gmane.science.biology.informatics.conductor/18 959/focus=18974 ... there you'll find discussion on i) apt tools (outside of R), ii) aroma.affymetrix, iii) oligo ... and another alternative is the 'xps' package. Hope that helps. Mark On 07/10/2008, at 4:47 PM, AMETS SAENZ PE?A wrote: > Hi, > > > > I have previously used R to analyse HG-U133A and B arrays and > everything was perfect. I like very much how I could see the PCA > plots... > > > > However, a colleague of mine has started using arrays "human gene > 1.0 st" and we found a problem when we wanted to analyse them. > > > > Dr Irizarry told me that this array is not supported in the affy > package, and that he thinks oligo package does. > > But he suggested me to ask in this e-mail. > > > > Thank you very much for your help. > > Waiting for your answer, > > > > Best regards, > > > > Amets S?enz > > > > > > Dra. Amets S?enz > > Unidad Experimental > > Hospital Donostia > > P? Dr Begiristain s/n > > San Sebasti?n 20.014 > > Tel: 943 00 70 61 > > FAX: 943 00 70 61 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852