The pd.xxx packages are build with pdInfoBuilder for use with oligo and are made from files directly obtained from Affymetrix you will need pd.mogene.1.1.st.v1 which is already provided at bioC. In other words, with this function you can create a CDF file from a platform design package and a CEL file. In this respect I think it *may* also be of interest to mention that within the 'aroma.affymetrix' project a function called 'PdInfo2Cdf' is made available, which allows you to generate an experimental CDF file from a pdInfo package and a auxillary CEL file for the same chip type. You can easily check this yourselves using the ReadCelHeader function from the library 'affxparser' on a sample v1.0 and v1.1 array (you can obtain these directly from Affymetrix). The mouse Gene ST cardridge (v1.0) array is square (1050cols x 1050rows), whereas the mouse Gene ST plate (v1.1) array is non-square (990cols x 1190rows). Indeed from experience I also know that you cannot use the unofficial, affymetrix-provided CDF of the cardridge Gene ST array (v1.0) for the analysis of the plate Gene ST (v1.1) array.Īlthough according to Affymetrix the content that is probed is identical between the two arrays, the dimensions of the arrays and the number of probes on the arrays are NOT identical. Next message: CDF file for Mouse Gene 1.1 ST Array.Previous message: CDF file for Mouse Gene 1.1 ST Array.CDF file for Mouse Gene 1.1 ST Array Hooiveld, Guido Guido.Hooiveld at wur.nl
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