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Macroarray data analysis - (Aug/31/2004 )

Hi, I have obtained mountain-like datas by the ArrayVision software, and it is making me so headache on how to completely analyze those data.Anybody there can give me some suggestion.

Thanks in advance.



Hi Wei:

Do not feel overwhelmed.
First you have to be sure you do your proper statistical analysis to find out your interesting genes.
Once you do that. Then look for groups of metabolic pathways or responses that are known may be afffected by your treatment. Then start generating lists of genes (somebody else's lists) and compare with your treatments. Once you detected something interesting, new or that does not make sense, then you can start sitting and considering writing your paper. Read several papers on your subject that used microarrays to address their issues and then decide what you like and dislike and try to start puting together the figures for your paper.
Ask the advice of a statistician for the analysis, doing it for yourself can be painful.
There are several free software on the net to do so.

Wish you luck.



Once you start microarray experiments, you will get tons of data. Without proper interpretation, they are just a pile of garbage. I think the person who does the analysis even with the help of specialized software needs to have some knowledge of bioinformatics, such as various databases, sequence search and blasting. If you don't have such knownledge, find someone who has. It will help a lot.


And there are a lot of pathway analysis softwares that help to interpret micrparray data.

I can think of PathwayAssist (desktop soft, has a database for data interpretation), Pathways Analysis (web-based, has a database), and Metacore (web-based, has a databse).



use Spotfire

it is THE BEST!!!

-Paul Shapshak, PhD-

TIGR Microarray suite is a good option for microarray data analysis.
It is OSI Certified Open Source Software.