To use dChip, you need to provide Affymetrix array data files (in CEL or DAT format, or use public dataset from NCBI GEO, Broad Institute or Affymetrix data resource center), and the CDF file (Chip Description File). CEL files contain summarized probe-level (Perfect match and mismatch probes) data of Affymetrix arrays. dChip software uses the CEL files for normalization and model-based expression value computation from probe level data.
If it is desired to read in cDNA array data, one may make an external data file with every two columns as the green and red channel intensities from one array (e.g. obtained from GenePix GPR file), and the read it in dChip by “Analysis/Get external file”. Then the normalization and high-level analysis may be performed.
Convert binary CEL files
[Note: The 5/26/05+ dChip version can directly read binary CEL files so the following conversion is not needed.] You may use this Affymetrix CEL file converting tool to convert the latest binary-format (Version 4) CEL file to the text-format (Version 3) CEL file so dChip can read. Affymetrix conversion tool will convert all CEL files in a directory from version 4 to version 3, while leaving the file name the same. You can check the CEL file size before (4Mb) and after (10Mb) to make sure conversion is done. Make sure the CEL files are not read-only (e.g. when copied from CD) before conversion. If conversion fails but you have DAT files, you can also ask dChip to read them instead of CEL files. To convert file format automatically, the GDAC file SDK may help.