does anyone have the information required to make the qcdef file for this more recent chip, or, better, a working qcdef file? to recall for the +2.0 we need array hgu133plus2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at thanks

I'm not sure simpleaffy is going to work with a PM-only chip, even if you do come up with a qcdef file, as it relies quite a bit on running (an internal C version of) mas5. Best, Jim James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 >>> Vincent Carey 12/22/10 7:21 AM >>> does anyone have the information required to make the qcdef file for this more recent chip, or, better, a working qcdef file? to recall for the +2.0 we need array hgu133plus2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_5_at ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX- HUMGAPDH/M33197_M_at thanks _______________________________________________ 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues