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Software for Microarray Data Analysis


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8 replies to this topic

#1 borriello.87

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Posted 24 August 2009 - 11:33 PM

Hi everyone,
Iím a medical student at the Second University of Naples and Iím going to use the Agilent DNA microarray scanner in order to perform my first microarray experiment.
Besides studying the protocols, Iíd like to learn how to analyze microarray data. Beacause I have no experiece in this field, does anyone of you know a free easy-to-use software for microarray data analysis?
Iíve heard about bioconductor, but maybe itís too difficult starting with itÖor not?


Thanks a lot

Francesco

#2 HomeBrew

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Posted 25 August 2009 - 03:04 AM

Hello borriello.87 -- welcome to the BioForums!

Bioconductor, which runs under the R statistical language, is your best bet for this. It's robust, well-tested, and widely accepted. Unfortunately, it's not that easy to use, at least initially.

It seems that with microarray analysis software, given "free", "powerful", and "easy to use", you get to pick two.

Does Agilent offer you anything in the way of analysis software?

#3 borriello.87

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Posted 25 August 2009 - 05:21 AM

Thank you for your answer!
As far as I know, Agilent offers GeneSpring GX as software analysis, but in order to use it you have to buy a license and my boss doesn't want to.
So I have to choose "free" and "easy to use", at least until I will learn to use a "powerful" analysis software like bioconductor.
Do you know any software with these features? And what about GenePattern? Do you know anything about it?

Thanks

#4 HomeBrew

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Posted 25 August 2009 - 02:10 PM

What type of microarray experiment are you doing (e.g. ChIP-on-chip, DNA Methylation, Gene Expression)? The type of experiment will determine the type of data output, which will determine what software is appropriate for analysis...

I have only done gene expression chips, and I used NimbleGen chips (mostly because they had an array already designed for my organism). I couldn't find much in the way of ready-to-go free software for my analysis of differential expression, so I wrote my own.

I also played around with SAM, and ran a few genelists through DAVID, but ultimately I wrote my own analysis program using, among other things, a method similar to rank products.

#5 noelmathur

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Posted 25 August 2009 - 10:26 PM

Also take a look at BRB Array Tools Its a great program and very good documentation. The support team is also very quick in responding your questions. Their forum is bit dated though. Still you can get your job done.

A warning about DAVID (or most of the GO tools), between 2002 and 2008, about 70 or so programs showed up doing Gene Ontology analysis. Most of them went remained as they were on the day of publication so are practically useless. Some programs like DAVID and Onto-Express are still getting updated and are good but in my feeling is both of them lack documentation so be prepared to wreak your head.

My honest recommendation to you would be, get someone do this work for you. You will save a lot of time and the person gets authorship on your article. Trust me, its worth it.

Don't get into this 'R' story, thats only for geeks, learning curve is steep (and be prepared to hear conflicting views in analysis. Learn to make informed decision)

#6 HomeBrew

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Posted 26 August 2009 - 03:49 AM

Also take a look at BRB Array Tools Its a great program and very good documentation. The support team is also very quick in responding your questions. Their forum is bit dated though. Still you can get your job done.

A warning about DAVID (or most of the GO tools), between 2002 and 2008, about 70 or so programs showed up doing Gene Ontology analysis. Most of them went remained as they were on the day of publication so are practically useless. Some programs like DAVID and Onto-Express are still getting updated and are good but in my feeling is both of them lack documentation so be prepared to wreak your head.

My honest recommendation to you would be, get someone do this work for you. You will save a lot of time and the person gets authorship on your article. Trust me, its worth it.

Don't get into this 'R' story, thats only for geeks, learning curve is steep (and be prepared to hear conflicting views in analysis. Learn to make informed decision)


The R statistical language's abilities are not in doubt. It gets knocked around for being difficult to use, but then again, so does the S language on which it is based, and which is used in commercial statistical apps like S-PLUS. There may be a module or two that uses suspect methods, but that's the beauty of open source -- if something is wrong with a module's approach, it gets pointed out and fixed, because others have access to the source. If you stick with the well-known modules, like those available hrough the Bioconductor project, you'll be on solid ground.

BRB Array Tools looks very nice as well. BTW, the statistical analysis it performs is based on -- you guessed it -- the R statistical language...

It is a good idea to bring in a collaborator familiar with microarray data analysis; there is a lot to consider to be sure what you're seeing is real and significant.

#7 noelmathur

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Posted 26 August 2009 - 04:49 AM

Totally agree with HomeBrew. Nothing is better than 'R' (I got to know 'S' just now) but the whole deal here is whats your goal? I seriously tried learning 'R' and the course coordinator flatly asked me what I want to do in future, do I want to end up as a Bioinformatician doing just dry lab or developing modules for large scale studies or I want to go biology way. He is (and now I am) of the same opinion, unless you want to build a career, it is waste to invest time on such steep learning.

Another caution, if you do get a collaborator. Make them see what you are seeing. Geeks don't understand biology very well so make them understand your hypothesis very well, before you let them touch your data. And DON'T ask them why certain gene is up or downregulated that you think should be the other way around, they don't know that. :lol:
(We have had really heated arguments on similar stuff in our department)

#8 Geno

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Posted 27 August 2009 - 12:57 AM

Have you heard about Genowiz™ a comprehensive microarray data analysis software package.
it supports variety of platform like Affymatrix, Agilent or your customized formats.

for more information click following link :

http://www.ocimumbio...c...&prodType=1


Please write to me directly if you need more information: manoj.b@ocimumbio.com

Manoj.B
Microarray Division
Gene Logic - Ocimum Bisolutions

#9 Sara Jackson

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Posted 20 October 2009 - 06:49 AM

Hi,

Please try BxArray software for Microarray analysis. This is web based, highly reliable, affordable and secure tool. Pl check the details on http://bioinforx.com...ct_bxarrays.php

KEY FEATURES of BxArray are as follows:

* Powered by BxAF technology.
* Supports multiple microarray platforms.
* Supports custom microarray analysis procedures.
* No previous knowledge of microarray data analysis is required.
* Contains advanced data analysis algorithms.
* Quick analysis with results ready in minutes.
* Customize analysis procedures to fit special procedures.
* Allow to download all analysis intermediate/final files and run analysis again locally.
* No programming is necessary but can also run custom analysis scripts.

You may also sign up for free to try the system. They are offering discounts- 3 Months Free Subscription for new customers and arrange special demonstration for your lab at your convenience.

If you have any questions, please do not hesitate to contact Bioinforx, Inc at info@bioinforx.com or at 608-467-4936

Good Luck!!




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