[BioC] last call for Boston bioc Training, 13-15 july, content revised

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Jul 6 20:02:01 CEST 2006

Limited spaces remain for the Boston course.

data analysis for high-throughput biology

open source approaches with Bioconductor

three day short course, Longwood Medical Area
July 13-15 2006

registration materials at

This course has a new structure/content.  Modules (to
be covered at a rate of approximately 3/day):

*Taster: Gene expression in airways hyperresponsiveness;
   annotation, gene set enrichment; transcript profiling
   in the yeast cell cycle; genetical genomics of human
   chromosome 20

*Interacting with R and Bioconductor: websites, packages,
   documentation, community

*Bioconductor: data structures and workflow components

*Microarray workflow: focus on affy$^{tm}$ expression arrays:
   CEL files + phenoData = AffyBatch; basic QC;
   spikein data and comparison of preprocessing methods;
   affyPLM; affylmGUI; other technologies

*Gene filtering: mechanics: closure of exprSet class under subsetting;
   subject-matter: ontology; pathways

*Exploratory data analysis (unsupervised learning):}
   general resources in R; visualization; distances, clustering, heatmaps;
   PCA, biplots

*Differential expression analysis (transcript profiling)

*Annotation resources: chip-specific mapping environments;
   probe sequence access; organismic metadata: YEAST; genomic sequences;
   systems biology resources: GO, KEGG, cMAP;
   specific web services: biomaRt, RSNPper, RMAPPER

*Methodology for functional gene set analysis

*Classification; supervised learning: distances;
   generalization error and discriminatory capacity;
   nearest neighbor methods; recursive partitioning and derivatives
   (random forests); boosting; svm

*Project: linking airways hyperresponsiveness arrays
   to genetical genomics resources


Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

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