[BiO BB] question about Agilent microarray data format

Alberto Pascual Montano pascual at cnb.uam.es
Tue Sep 5 04:38:45 EDT 2006

Hi James,

You can download the manual for the Agilent Feature Extraction software at:


There you will find details of the data format. In summary, "gProcessedSignal" "rProcessedSignal" are the Cy3 and Cy5 processed signals (the normalization algorihtms used are described in the data file), "LogRatio" is the base10 log ratio (rProcessedSignal/gProcessedSignal) and PValueLogRatio is the significance level of the calculated log ratio.


----- Original Message ----- 
  From: James Anderson 
  To: bio board 
  Sent: Friday, September 01, 2006 9:03 PM
  Subject: [BiO BB] question about Agilent microarray data format

    I have some Agilent microarray data. I am not familiar with the format. (I am more familiar with Affy data). There are some columns named "gProcessedSignal" "rProcessedSignal", "LogRatio", etc. I guess it's more like cDNA with two channels. So should I use the LogRatio value to perform the next step analysis (gene selection, PCA, clustering, etc).  


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