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Re: Microarray data analysis

  • To: mathgroup at smc.vnet.net
  • Subject: [mg125084] Re: Microarray data analysis
  • From: Matthias Odisio <matthias at wolfram.com>
  • Date: Tue, 21 Feb 2012 06:09:55 -0500 (EST)
  • Delivered-to: l-mathgroup@mail-archive0.wolfram.com
  • References: <jh2tae$qf$1@smc.vnet.net> <201202200743.CAA24057@smc.vnet.net>

Dear Karthikuttan,

On 2/20/12 1:43 AM, karthikuttan at gmail.com wrote:
> Thanks for your reply. I will explain what I need in detail this time.
> 
> What I have is Agilent single-color microarray analysis data files extracted using Agilent feature extraction software (AFE). I ahve TIFF, JPEG and TXT files from AFE. I want to know if mathematics comes with a built-in tool that can accept the above mentioned TIFF image and work on it. If Mathematica can accept the TIFF image, does it also accepts the Grid information file for the TIFF microarray image so that it can find out XV co-ordinates etc.? IF so where can I get the grid info file for my Agilent microarray chip?
> 
> I am not sure, if mathematica can do all these things, what kinds of analysis will it perform over the TIFF file and what will it give as output and in what format? Is it going to be a text file containing probe intensity values? If yes, can I import this output file from Mathematics into GeneSpring?
> 
> I know I am asking too much questions at once. But, pardon me, because these things have been eating my head for a long time and still I could not figure out  a way to analyze the Agilent TIFF file. AFE is of course an options, but I would  like to get more significant results by putting more than one software.
> 
> Thanks a lot.
> 

Do you think you could share your files with us? I would be happy to
put out a solution for your needs. Most probably we won't run into
much troubles, but I'd rather make sure we come up with a working
example at once.

Matthias Odisio
Wolfram Research



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