Hello, Does anyone know if I can calculate the signal value implemented in Microarray Suite Version 5.0 using affy. If so what is the function call to this? I tried to use mas5calls.ProbeSet but the signal value is not same as that generated by the Microarray Suite Version 5.0 software. If affy doesn't do it does anyone know of a package that does within the bioconductor project? Many thanks. Ruppert

Hi Ruppert, mas5calls.ProbeSet doesn't give you the signal values, but instead gives the present/marginal/absent calls. If you want the signal values, the affy vignette says to use: eset <- mas5(affybatch.example) I would also check to make sure the same scale value was used in both cases... Our core center typically scales to a mean value of 300 units, where as the default for mas5 is 500 units. HTH, Jenny At 08:29 PM 3/14/2006, Ruppert Valentino wrote: >Hello, > Does anyone know if I can calculate the signal value implemented in >Microarray Suite Version 5.0 using affy. If so what is the function call to >this? > >I tried to use mas5calls.ProbeSet but the signal value is not same as that >generated by the Microarray Suite Version 5.0 software. > >If affy doesn't do it does anyone know of a package that does within the >bioconductor project? > >Many thanks. > >Ruppert > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu