Seminar 8: Edit methylation seminar
Edit seminar 08 methylation
Assign hw02; add hw02 data

more questions to be posted ...
Seminar 7: Fix the call to estimateGLMTagwiseDisp

estimateGLMTagwiseDisp needs the model matrix.

Closes jennybc/stat540-devel_2014#25
Add seminar 09
Edits to seminar09_clustering-pca

 * many changes to follow conventions, tidy code, correct typos
 * some to make code more robust
Use variable names when plotting; fixes an error for me
Link to seminar09_clustering-pca
Add RNA-Seq data for hw02
Add question 2 to hw02; deals with the RNA-Seq data
Sanity check / demo what row rescaling does
Use interaction() to create factor representing interaction gType and devStage; remove car package from dependencies
Expose package loading
Discipline re: saving and restoring graphical parameters set via par()
Tidy heatmap() calls; set up colours for devStage

If want default args, don’t specify. More/better use of arg names.
Use conventional k to specify number of clusters; use same approach to tabulate devStage by cluster for PAM and k-means
Add exercise
Refactor clustering based on averages expression within devStage

The plyr way isn’t shorter, but seems better to model. I suspect we should really be exploiting reshape2 here.
Delete unnecessary par() fussing
Link to PDF slides for lect16_cluster-analysis and lect17_supervised-learning