- February 16, 2010
Next -generation sequencing symposium - December 7, 2009
Affymetrix User Group Meeting
Please see our acknowledgment policy.
- Statistical Consulting Service Overview
- Genetic Analysis
- Microarray Gene Expression Analysis
- Copy Number Variation Analysis
- Next Generation Sequence Data Analysis
- Genome-wide Epigenetic and Epigenomic Analysis
- Other Data Types
- Statistical Analysis Tools/Software
- Statistical and Software Training
- Statistical Analysis Pricing
- Support Letter
- Publications by Statistical Facility
- Facility Contact
The TCAG statistical consulting service can provide a wide range of advice and assistance:
- advice on study design and analytical planning
- sample size and power calculations
- statistical analysis of study data
- interpreting and summarizing results
- assistance for writing grant proposals.
We focus on methods applicable to the types of data produced within the facility, including:
- Genetic analysis
- Microarray gene expression analysis
- Analysis of copy number variation
- Next generation sequence data analysis
- Genome-wide epigenetic and epigenomic Analysis
We are always interested in expanding our knowledge into new data types.
- Design and analysis of genetic linkage mapping studies
- single gene disorders or complex diseases
- discrete or quantitative traits
- evaluation of covariate effects on linkage signals
- mapping in natural or experimental crosses
- Association studies of quantitative and discrete traits
- family-based control design
- case-control design
- population stratification
- single marker or multi-marker associations
- genome-wide association analysis
- Estimation of haplotypes in related or unrelated individuals
- Power calculations
- Experimental design
- sample size and power calculations
- Analysis of data from various platforms (e.g. Affymetrix, exon arrays, Illumina, others)
- pre-processing (normalization, filtering, QC metrics, visualizations, etc.)
- identification of differentially expressed genes
- time course studies
- multiple experimental factors and/or interactions
- clustering and class prediction
- limited pathway and gene function analysis
- Multiple hypothesis testing (e.g. control of false positive and false negative rates)
- MicroRNA data analysis
- Alternative splicing data analysis
- Data integration across platforms and laboratories
- Analysis of data from different platforms (aCGH, BAC or Agilent oligonucleotide arrays, Affymetrix/Illumina SNP arrays)
- Identification of regions containing copy number changes
- Testing for differences in frequency of copy number changes between groups
- Alignment, genome assembly, genome annotation, etc.
- Variant detection (SNPs and structure variants)
- Identification of enriched regions
- Differential analysis of transcript read counts for expression profiling
- Design and power analysis of epigenetic/epigenomic studies
- Identification of epigenetic/epigenomic signatures
- Chromatin mapping
We can provide advice and perform analysis for a wide variety of other data types not listed above. Some examples are:
- Annotation of uncharacterized gene functions
- Enrichment analysis of gene sets
- Pathway analysis
- Proteomic data
- Epidemiological studies
Please contact the facility for details.
We use the tools and software which include state-of-the-art, well-compared, widely-adopted and transparent methods for data analysis. Examples of these can be found at www.bioconductor.org, http://www.nslij-genetics.org/soft/ and http://probability.ca/cran/.
We have installed Matlab on our cluster (http://www.ccb.sickkids.ca/hpf_index.html) with the following major toolboxes:
MatlabBioinformatics
Statistics
Optimization
Parallel Computing
8 distributed Servers
Users who would like to use this software will be required to pay a project-based or an annual based fee. Pease contact the facility for details.
In addition, we have a series of commercial software for different types of data analysis: GeneSpring, SpotFire, Stratagene, Partek and Ingenuity Pathway Analysis, etc.
We provide statistical and software training primarily in one-to-one or small group (e.g. from a specific lab or project) settings. We provide tutorials or workshops for specific approaches and software to larger groups as needed. For more information, please contact the facility.
The Statistical Analysis Facility provides consultative services at varying rates depending on project scope:
- hourly basis: $70 per hour
- Weekly or monthly basis. Applicable for long term projects requiring dedicated personnel (e.g. genome-wide association analysis). Please contact the facility for details.
Download the Statistical Analysis Consulting Form.
For a free initial consultation and estimate, please contact the facility.
We will gladly provide investigators with a letter of support stating our willingness to assist you in grant applications. Please contact the facility.
- Study design
- Sample size and power calculation
- Write statistical analysis plans
- Provide a letter of support
- Selected methodology publications by Statistical Facility staff
- Selected publications by Statistical Facility users (Co-authored or Acknowledged)
The Hospital for Sick Children
MaRS Centre - East Tower
101 College Street, Room 15-705
Toronto, Ontario
M5G 1L7, Canada
Tel.: (416) 813-7654 ext. 6016 Fax: (416) 813-4931
Email: