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Old 04-05-2010, 10:19 PM   #1
BioSlayer
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Default MicroArray and Sequence Analysis

Dear Fellows, I am a Perl programmer and good in Biology too, however, I am very interested to know more about Sequence analysis and microarray data analysis, I have gone through the forum, but I think for a NOOB like me, I gotta probably start from scratch and connect everything together, I am not bad in statistics too, worked as a SAS programmer for sometime (Clinical trials), however, we don't have SAS out here....

My inquiries are:
  1. What are the routine statistical must-knows techniques in the field of microarray data analysis and next generation sequence analysis?
  2. Software or platforms that you recommend to use in gene assembly, mapping...etc - put another way - directions into the various tasks that come with sequence analysis and microarray design and analysis that I need to master as a bioinformatician (I would really appreciate these directions dearly).
  3. Generously, suggest me any links that can be useful for a self-education based approach to develop

Other than that, I would like to contribute back, in the long run, probably by providing Perl libraries to automate some of the interesting tasks that we'd get to do day to day...

Thanking you ...

Last edited by BioSlayer; 04-05-2010 at 10:24 PM. Reason: Clarified some points
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Old 04-06-2010, 05:56 AM   #2
NextGenSeq
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IMHO, microarrays are going the way of BAC cloning. Everyone will be due transcriptome sequencing soon.

The best way to learn the NGS field would be to download software and data and work with it.
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Old 04-06-2010, 07:03 AM   #3
krobison
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Look through the BioConductor website; there will be vignettes there for most of the tools.

Microarrays will be take a while to tail off & won't be at a total disadvantage (still cheaper at the moment) for at least a year. A lot of the techniques will carry over.

Wonder when I'll see my first appalling RNA-Seq experimental design to join the legions of horribly designed microarray experiments.
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Old 04-06-2010, 09:53 AM   #4
NextGenSeq
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Isn't BioConductor only for microarray data? I use GeneSpring so have never used it.

For Next gen sequence analysis look through the sticky "Software packages for next gen sequence analysis" at the top of this thread.
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Old 04-06-2010, 05:58 PM   #5
krobison
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There are a number of BioConductor packages which are either agnostic about the type of data or are specifically for 2nd gen sequencing data (e.g. DEGseq for RNA-Seq; ShortRead is general set of classes).


Also, it would be supremely foolish to not learn the lessons learned over a decade of microarray analysis, as very many of the same issues will be faced or analogous issues arise (e.g. correcting for multiple testing)

Don't forget the software wiki! It is likely to be less incomplete than the thread.
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