[BioC] simpleaffy qcdef for hugene 1.0 st?

James MacDonald jmacdon at med.umich.edu
Wed Dec 22 14:24:35 CET 2010

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.



James W. MacDonald, M.S.
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
>>> 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


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