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dChip for Gene Expression and SNP Microarray Data Analysis
Boston, Massachusetts
January 26-28, 2009
http://wiki.bioinformatics.org/BI201C_dChip
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(Please share this with others who might be interested.)
The Bioinformatics Organization (Bioinformatics.Org) will hold a 3-day workshop
on gene expression analysis and SNP microarray data analysis using the dChip
software (www.dchip.org) developed by Harvard University Associate Professor
Cheng Li.
This hands-on course in Boston will teach the workings of the dChip application
and cover topics such as importing arrays, performing normalization, model
based expression calculations, gene and SNP filtering, clustering, linkage, LOH
and copy number analysis.
COURSE OUTLINE:
Session 1: Gene Expression Analysis: Preparing to import CEL and CHP exported txt files,
with basic actions such as normalization and model-based expression index calculations.
Re-importing saved "DCP" files and importing expression indices from saved text
files. Use of array list file, sample information file, dChip data file list.
Session 2: Gene Expression Analysis: Case studies with comparison of two
groups, gene filtering and clustering
Session 3: Gene Expression Analysis: Case studies with ANOVA, correlation,
enrichment and classification
Session 4: Gene Expression Analysis: Resampling, manipulating trees, gene
function enrichment, pathways, FDR, combine comparisons
Session 5: SNP Array Analysis: Preparing to import CEL and CHP exported txt files, with
basic actions such as normalization and model-based expression index calculations for
copy number analysis; re-importing saved "DCP" files and importing genotypes
and SNP signals from saved text files; use of array list file and sample information file.
Session 6: SNP Array Analysis: LOH and copy number analysis with sample data;
export.
Session 7: SNP Array Analysis: Intricacies of copy number and LOH analysis,
parameters used
Session 8: SNP Array Analysis: Allele sharing analysis, linkage analysis; automation in dChip
INSTRUCTORS:
Prof. Cheng Li, Dana Farber Cancer Institute and Harvard School of Public
Health, author of dChip
Shailender Nagpal, Bioinformatics Organization and Tanisha Systems
FOR MORE INFORMATION:
http://wiki.bioinformatics.org/BI201C_dChip
(Course TAA)
Cheers,
Jeff
--
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: [email protected]
Phone: +1 978 562 4800
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