Editing BioMicroCenter:MicroArrays (section)

== Analysis and Data Retrieval ==

=== Affymetrix Data Analysis ===

BioMicro Center will perform the initial data extraction of your samples using Affymetrix GCOS V.1.4. Affymetrix data is scaled to a average intensity of 500 per chip. Six files for each sample will be sent back to the user:

* .exp: Experiment information file 
* .dat: The image of the scanned probe array.
* .cel: Cell Intensity File derived from  .dat file. 
* .chp: Output file generated from the analysis of a probe array.
* .rpt: Report File generated.
* .txt: Text File is the same information as the .chp file in text format.

Additional data analysis help is available on a case by case basis. Please contact [[BioMicroCenter:People|Stuart Levine]] if you need additional help with your analysis.

=== Data Transfer ===

You will be notified by email that your data is ready. At that time please pick up any leftover samples and arrays belonging to you. Samples will be held at the facility at -80C for 60 days after your data is generated. 

The data will be placed on our server and can be downloaded by SFTP.
Your user name and password will be included in the email. To obtain your data, enter the following in your client: 

  Host:       bmc-150.mit.edu
  user:       provided in email      
  Password:   provided in email

Please contact [mailto:bmc-data@mit.edu bmc-data@mit.edu] if you have difficulty obtaining your data.