GenePix Tips

• The ArrayFun and BACarray packages are designed to start with data from a GenePix scanner.  Use GenePix software to produce raw data (.gpr) files. 
• It is recommend that you set a minimum spot diameter in GenePix settings in order to flag missing spots.  The opmtimal spot diameter will depend on the array platform and will need to be determined emperically. 
• GenePix settings should be saved and and then used to process all of the images from a single experiment similarly in batch mode. 
• Inspect spot alignments to be sure that there are correct.  Manually flagging bad spots can be done but should not be necessary on clean arrays.
• Further processing  of the .gpr data is then done within R.  Do not use .gpr files which have been filtered or background subtracted by other applications and do not use .gpr files whish have been openened and saved with Microsoft Excel.