Hi, I am using custom CDF file for my rat gene chip 1.0ST arrays (n=115). I got the following when I used SimpleAffy's qc Could not find array definition file ' ragene10stv1cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. I followed the instructions I found and got the following file made and saved as ragene10stv1cdf.qcdef and placed it in R library folder array ragene10stv1cdf alpha1 0.05 alpha2 0.065 ratio actin3/actin5 AFFX_Rat_beta-actin_3_at AFFX_Rat_beta-actin_5_at ratio actin3/actinM AFFX_Rat_beta-actin_3_at AFFX_Rat_beta-actin_M_at ratio gapdh3/gapdh5 AFFX_Rat_GAPDH_3_at AFFX_Rat_GAPDH_5_at ratio gapdh3/gapdh5 AFFX_Rat_GAPDH_3_at AFFX_Rat_GAPDH_M_at then the following setQCEnvironment("ragene10stv1cdf", path="/Library/Frameworks/R.framew ork/Versions/2.13/Resources/library") the error was qc(data) Error: NAs in foreign function call (arg1) Where am I going wrong? Rizwan