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Re: Microarray data analysis

  • To: mathgroup at smc.vnet.net
  • Subject: [mg126902] Re: Microarray data analysis
  • From: Karthu <karthikuttan at gmail.com>
  • Date: Fri, 15 Jun 2012 15:32:58 -0400 (EDT)
  • Delivered-to: l-mathgroup@mail-archive0.wolfram.com
  • References: <jh2tae$qf$1@smc.vnet.net> <201202200743.CAA24057@smc.vnet.net> <jhvu4d$800$1@smc.vnet.net>

Thanks everyone and so sorry to reply to this post very late.

After much thought, for now, I have decided not to do anything with the TIFF image. I am very happy that Matthias offered me his expertise on this issue. I will definitely comeback to this in future.

For now, I will be glad if somebody could help me analyze the microarray data that I have in txt format (Microarray I used, as I said earlier is Agilent platform). I found one post regarding gene expression analysis using mathematica, but could not get much from it.

Is it possible to do normalization, filtering out probes that doesn't satisfy 'flags' etc in Mathematica? I would be glad if someone could help me by providing detailed manuals ( and text-based or video-based tutorials. Pre-made codes will be excellent as I am very new to Mathematica.

Also, I am interested to know about the possibility of Mathematica-R integration . Since there are many Bioconductor packages for microarray analysis, accessing the R/Bioconductor capabilities from Mathematica will be just "cool". I know of RLink, but it is expensive. I would rather look for some open-source applications, if available.

Thanks a lot once again,

Looking forward to receive some help and suggestions/comments.

Karthik

On Tuesday, February 21, 2012 4:41:09 PM UTC+5:30, Matthias Odisio wrote:
> 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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