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SOM and clustering for gene array analysis (Affymetrix) in perl

by dondelelcaro (Monk)
on Sep 06, 2001 at 16:27 UTC ( #110547=perlquestion: print w/replies, xml ) Need Help??
dondelelcaro has asked for the wisdom of the Perl Monks concerning the following question:

I am going to be analyzing a large number of gene arrays fairly soon (I leave for NY on sunday), and have spent a bit of time researching some of the clustering algorithms that are out there. It seems that I am going to have to roll my own right now to do exactly what I want, but as I'm not the best at algorithmic development {my name isn't Knuth}, I was wondering if any monks out there have had experience (or knew of projects) dealing with clustering and self-organizing maps, or even importing affymetrix data into a useable format.

I'm in the midst of sorting through the vast assortment of google'd information out there, but was wondering if some of you could point me to code/algorithms that I really should be looking at. (And even if you don't know of some, I'd love to here from monks who are using perl to do bioinformatics, specifically gene array analysis {I normally do other "bioinformatics" things, but this project needs doing ;-)})
  • Comment on SOM and clustering for gene array analysis (Affymetrix) in perl

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Re: SOM and clustering for gene array analysis (Affymetrix) in perl
by DigitalKitty (Parson) on Mar 04, 2007 at 23:07 UTC

    Assuming you're using R, I suspect you'll enjoy bioconductor. Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. It's an immensely powerful tool for those working in the field of computational biology / biomedical research.

    Hope this helps,
Re: SOM and clustering for gene array analysis (Affymetrix) in perl
by byronellis (Novice) on Sep 07, 2001 at 01:11 UTC

    <shameless plug>If you want to array analysis and cluster you might want to try dChip ( It's not written in Perl and it runs on Windows but people seem to like it :-) (I didn't write it, but the guy who did is in my lab).</shameless plug>

    Actually, we do a lot of microarray stuff (mostly Affy, some cDNA) using, among other things, Perl and R. Which affy files were you interested in parsing?

Re: SOM and clustering for gene array analysis (Affymetrix) in perl
by kathy2009 (Initiate) on Jun 12, 2009 at 03:21 UTC
    I am trying to analyze the affymetrix data, which files I should analyze : *.DAT, *.CEL or *.CHP or else. and how? Can any one give me more detail suggestion? How to use in dchip or R?

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[Discipulus]: your cat is dryarian holli
[holli]: not even remotely KurtZ. i did find feathers in the garden a few times though
[holli]: yet no body
[virtualsue]: I was called upon to remove a gnawed mouse carcass from the living room this morning
holli googles dryarian just to make sure that isn't actually thing
[holli]: I mean, you never know, right?
[shmem]: good $localtime monkses
[holli]: mmh. maybe a user handle "dry arian" is a bit unfortunate? https://www. dryarian/
[Discipulus]: exists!
[shmem]: holli, agreed. "dry airan" would be slightly better :P

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