Normalize the data

Background subtraction:
Next thing that you are asked is, if you want to subtract local background: press "yes" or "no".
Normalization:
- In the next menu you choose the type of normalization, if you have no idea about that:
  just click the "smiley-button".
- This is also true for some further selections.
- In the next menu you choose the normalization method.
- Now a lot of scatter plots and accompanying correlation coefficients appear and you can have a look at them either in a logarithmic or linear scale.
- To speed up the further analysis process, it may be good to "close them all".
- Then you are asked if some hybs showing a bad correlation coefficient (< 0.8) should be discarded:
  type in your cut off value for the correlation coefficient.
- It is written, which measurements are discarded.
- You can decide, if you want to re-normalize or not.
- Now you have the possibility to save your normalized dataset; e.g. "name_of_saved_file"
  (they are automatically saved in a ".mat"-format; if you want to reuse this file,
  - Start matlab
  - >> load name_of_saved_file
  - >> cont
  and analysis will continue exactly at this point).
- After this, a menu line ("File, Edit, View, Analysis, Database, Help")
  will appear where you can choose different kinds of analysis, filters, etc.

Please find more information about M-CHiPS normalization in the FAQs or under the headings Data analysis --> Preprocessing --> Normalization at http://kups.ub.uni-koeln.de/volltexte/2003/364/pdf/11w1296.pdf