[BioC] SimpleAffy qc step for custom CDF files

[Ahmed, Rizwan]

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.framework/Versions/2.13/Resources/library")

the error was
qc(data)
Error: NAs in foreign function call (arg1)

Where am I going wrong?

Rizwan