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 on January 26-28, 2009 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.
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
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