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Old 07-24-2010, 04:15 AM   #1
BioSlayer
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Default Pathway Analysis packages for microArray

We're using a microarray platform from Agilent for a cancer study, and we're interested in analyzing data from SNP, gene expression copy number variations via Comparative Genomic Hybridization (CGH-arrays) perspectives, the analytical goals involve:
  1. Pathway Analysis
  2. Feature Extraction
  3. Miscellaneous analyses

In our quest to acquire specialized software I have looked into GeneSpring and the Ingenuity Pathways analysis (IPA) in addition to Partek (Genomic Suite) but still I need assistance in recommending to me what other alternative vendors out there I should include in analyzing the requirements and the cross functionalities offered by each one of these solution for our analytical goals.

I am resorting to the wiser fellows at seqAnswers to guide me around by their generous contributions..

Thank You...
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Old 07-24-2010, 05:31 PM   #2
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Hi Bioslayer,

If you need extensive and customized analysis, most likely not a single software or software package can satisfy all your needs. You may consider professional consultants - I am one of them - check www.contigexpress.com.

Good luck,
Douglas
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Old 07-24-2010, 10:06 PM   #3
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Hello Douglas,

Thanks, we're just analyzing these applications so far, while some of these packages are specialized at a given genomic activity, others are more generalized whereas yet there are other packages which are publicly available...

So I am just trying to collect many of the different packages out there and study their specs, features, price and measure that against our requirements..
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Old 07-25-2010, 06:13 AM   #4
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In that case, CLC Bio genomics workbench also includes general microarray analysis modules: http://www.clcbio.com/index.php?id=1240
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Old 07-25-2010, 11:22 AM   #5
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Exactly, So I included CLC BIO together with other 9 vendors like agilent and Geospiza and we're trying to compare different areas that each one of these is going to fit in..
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Old 07-25-2010, 11:17 PM   #6
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Hi BioSlayer... hopefully by now you must have compiled the list. Can you please share it with other users...
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Old 07-27-2010, 05:29 AM   #7
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We've approached the following companies, while this list is yet not so exhaustive, however, some of these vendors products can be comparable, we're yet to find out after coming in contact with their sales agents and waiting for their response to our queries...
  • agilent.
  • ingenuity (Pathway Analysis).
  • Aridane Genomics.
  • GeoSpiza.
  • Partek.
  • Tibco (Spotfire).
  • Biobase.
  • Ocimum Biosolutions.
  • GeneGo metacore (Pathway analysis).

The web addresses to these companies are readily available and we're still yet to analyse our needs a little bit further.
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