Microarrays
===============

Animation of a typical experiment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

http://www.bio.davidson.edu/courses/genomics/chip/chip.html

You tube video, microarrays for comparing infected and uninfected plants:
http://www.youtube.com/watch?v=VNsThMNjKhM


Resources (lectures and labs):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

`Introduction to Microarrays using BioC: <http://www.sbforum.org/cmsimages/presentations/BioC.pdf>`_

`Keith Baggerly and Kevin Coombes <http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures05/ma07_bw.pdf>`_

`Baggerly and Broom, Data structures and BioC <http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/ma07b.pdf>`_

`Hao Wu slides from course: <http://userwww.service.emory.edu/~hwu30/teaching/bioc/GE.pdf>`_

`Normalization Slides by Brandon Higgs: <http://www.binf.gmu.edu/jafri/binf636/Normalization.pdf>`_

`VSN Normalization, motivation <http://www.bioconductor.org/help/course-materials/2006/biocintro_oct/lectures/M2ColorsAnalysis-Oct06.pdf>`_

`Quality control and design, with details about vsn <http://compdiag.molgen.mpg.de/ngfn/docs/2005/sep/beissbarth_cDNA_QCPP.pdf>`_

`Thomas Girke <http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Microarray/arrayBasics.pdf>`_

`Comparison of Methods (Baggerly and Coombes): <http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures05/ma14b.pdf>`_

`Example of a Lab Analysing Estrogen Data <http://www.bioconductor.org/help/course-materials/2005/BioC2005/labs/lab01/estrogen/>`_

`Example of a Lab covering RMA gcRMA by James Wettenhall: <http://bioinf.wehi.edu.au/marray/ibc2004/lab2/lab2.html>`_