It is optional but recommended to specify a “ Gene information file” for the current array type. Such custom CDF file can also be constructed for Nimblegen arrays and used in dChip to analyze the correctly formatted CEL files for Nimblegen arrays.
Only the probes in the custom CDF file will then be useful for normalization and expression computation. The header sections and are copied from the standard CDF file but the “NumberOfUnits” is changed to the number of probe sets that the custom CDF file contains. Use this attribute only for string type parameters that contain. Component Description Format User Guide: parseAsNumber specifies whether this parameter can evaluate to a floating-point number. You have to edit your NMOS CDF and add it to the paramter 'wtry'. A file can have name such as “HG-U133_Plus_2_dchip_example.cdf”, where “_dchip_” in the file name identifies dChip specific CDF format, the string before it identifies the original array type so dChip can search the corresponding CEL files, and the string after it can be anything for user’s own identification. I guess the CDF atribute 'parseAsNumber' for your parmater 'wtry' will do the job. >In general, you need to run a CDF file through the makecdfenv package >(using either () or ()) before it. dChip can read in a custom CDF file in dChip specific CDF format. Basically I got the CDF file in ASCII format and now trying to create a CDF package that I can use to analyse chips which are mixture of U133 and U95 (not good idea due to a lot of variation but I have to do it).
Sometimes it is desirable to reorganize probes in an array type i nto custom probe sets and compute expression values for them.
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