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<DIV><FONT face=Arial size=2>Hi James,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>You can download the manual for the Agilent Feature
Extraction software at:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><A
href="http://microarray.onc.jhmi.edu/forms/ImageAnalysisManual.pdf#search=%22Agilent%20Feature%20Extraction%20software%20%22">http://microarray.onc.jhmi.edu/forms/ImageAnalysisManual.pdf#search=%22Agilent%20Feature%20Extraction%20software%20%22</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>There you will find details of the data format. In
summary, <FONT face="Times New Roman" size=3>"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.</FONT></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards,</FONT></DIV>
<DIV><FONT face=Arial size=2>Alberto</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>----- Original Message ----- </DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=janderson_net@yahoo.com href="mailto:janderson_net@yahoo.com">James
Anderson</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A
title=bio_bulletin_board@bioinformatics.org
href="mailto:bio_bulletin_board@bioinformatics.org">bio board</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, September 01, 2006 9:03
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [BiO BB] question about Agilent
microarray data format</DIV>
<DIV><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><FONT
face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR></DIV>Hi,
<BR> 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). <BR><BR>
Thanks,<BR> James<BR>
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