[BioC] Calculating signal value implemented in Microarray Suite Version 5 using affy

[Jenny Drnevich]

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