[BioC] SimpleAffy qc step for custom CDF files
rizwan.ahmed at csc.mrc.ac.uk
Sun Aug 28 19:21:32 CEST 2011
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
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
the error was
Error: NAs in foreign function call (arg1)
Where am I going wrong?
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