Category Archives: Links

Python is cool.

Some Python links: http://pycogent.org/ http://nbviewer.ipython.org/ http://nbviewer.ipython.org/github/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/blob/master/Chapter1_Introduction/Chapter1_Introduction.ipynb https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks Advertisements

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What I’m Reading This Week

A blog that I read (Molecular Ecologist) has a Friday post almost every week about what they’re reading. I enjoy hearing about what other people are reading. It gives me ideas. These are some of the things I’ve been reading … Continue reading

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Raw Microarray Data Distribution Analyses – MA plotting

http://en.wikipedia.org/wiki/MA_plot http://cran.r-project.org/web/packages/EMA/vignettes/EMA_vignette.pdf http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Microarray/arrayBasics.pdf http://bioinformatics.oxfordjournals.org/content/18/4/576.full.pdf http://bioinformatics.oxfordjournals.org/content/25/3/415.full http://www3.it.nuigalway.ie/agolden/bioconductor/version1/MicroArrayAnalysis.pdf http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&ved=0CDsQFjAC&url=http%3A%2F%2Fwww.cs.princeton.edu%2Fpicasso%2Fmats%2Fmicroarray_analysis_basics_F08&ei=atFYUuKHOYSE9QSl4oDwDg&usg=AFQjCNGEIzdK6iTxhhB2-8xWCMoYPkbp8A&sig2=M5QRF3J3GtQquc-PnPVsKQ&bvm=bv.53899372,d.eWU http://www.bioinformatics.wsu.edu/bioinfo_course/notes/Lecture16.pdf http://www.biology.gatech.edu/people/pdf/gibson.MetEnz.pdf http://www.horizonpress.com/cimb/v/v4/06.pdf http://cri.uchicago.edu/wp-content/uploads/2012/05/Analysis-of-Microrrays-with-R-and-Bioconductor.pdf http://www.bioss.ac.uk/~dirk/lectures/gti_jan04/papers/shannon_clustering.pdf http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=8&cad=rja&ved=0CGQQFjAH&url=http%3A%2F%2Fwww.people.vcu.edu%2F~mreimers%2FHTDA%2FMicroarray%2520Quality%2520Assessment.ppt&ei=-tFYUsjRH4qY9gT7qIDgCg&usg=AFQjCNHPlLvQgZ_BMQg-gWMi_uKY4I76pQ&sig2=GEzbwcGNcbFHvJZMgsx6sw&bvm=bv.53899372,d.eWU http://www.pmean.com/99/arrayImport.htm Bioconductor: http://www.bioconductor.org/packages/2.12/bioc/vignettes/limma/inst/doc/usersguide.pdf http://www.sbforum.org/cmsimages/presentations/BioC.pdf http://www.bioconductor.org/help/course-materials/2008/BioC2008/labs/arrayQA/

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Permutations

Combinations of items, order matters: import itertools http://docs.python.org/3.3/library/itertools.html#itertools.permutations http://en.wikipedia.org/wiki/Permutation

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How To Get Help

Dr. Roger Peng’s intuitive set of instructions for how to properly ask questions on a programming forum is quite entertaining and informative: His video presentation was inspired by this: http://www.catb.org/esr/faqs/smart-questions.html

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