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ProCAT is a web tool that analyzes
protein chip
data and reports positive hits on the chip. The current version of ProCAT can deal with a typical protein
array experiment which may contain negative controls or protein amount normalizations.
Here is a list of functions included in the current version of ProCAT.
1. Background normalization that deals with the smears
2. Foreground normalization that deals with spatial artifacts
4. Protein amount normalization.
5. Analyze up to two probings together
6. Analyze Up to two negative control probings
7. Annotation from SGD for yeast proteome arrays
Protein chip can have very different formats. ProCAT requires the protein chip has following properties:
1. Foreground normalization may only work for dense protein arrays
2. Each protein is spotted in duplicate on slide
3. Protein names can be differientiate from the control spots on the array
4. All the obvious smears and bad spots are flagged out before analysis
5. Prefer gpr file generated by genepix as input data. Can use other file formats if proper parameters are inputted
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