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| Core Requirements for Statistical Analysis of Microarray Data Sets Cancer Stem Cell Program Statistical data analysis for experiments in the Cancer Stem Cell Program is available by contacting Biostatistician Changjiang Xu at changjiang.xu@utoronto.ca. In order to ensure that appropriate analyses can be performed and all relevant information is provided, the following guidelines would be followed 1. '''Required Laboratory Information''': a complete and concise information about the experiment, including the following |
##Core Requirements for Statistical Analysis of Microarray Data Sets ##Cancer Stem Cell Program Statistical data analysis for experiments in the Cancer Stem Cell Program is available by contacting Biostatistician Changjiang Xu at changjiang.xu@utoronto.ca. In order to ensure that appropriate analyses can be performed and all relevant information is provided, the following guidelines must be followed. 1. '''Required Laboratory Information''': a complete and concise information about the experiment, including the following |
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| - Animal strain (i.e. A/J mice) - Tissue/sample (i.e. lymphocytes) - Data type (i.e. gene expression data) - Chip used, along with version, - Day/Date when the experiment was conducted, o If different samples were analyzed on different days, a list of which samples were analyzed on which days is needed. o The experimental layout of the study, i.e. which samples are located where on the chip results (tracking worksheet for the experiment) [if relevant] - Explanations for the column labels used in the raw data files (see #2) - Copy of Tracking worksheet for your experiment 2. Raw data files should be in comma delimited (.csv) format (or in case of affymetrix .CEL files and CDF file to decode each .CEL file). a. No comment fields in the data b. Exactly one header line, naming all the columns using variable names that do not contain any spaces or underscores. c. A relevant set of row labels (e.g. probe_ids) d. Also provide the annotation file if your lab has prepared any special file 3. A short description of the experiment’s goals, clearly stated. This should include primary and secondary objectives, etc. Proposed Plan of Analysis, if biologists have any particular technique in mind, and the biological rationale behind that choice. Otherwise the biostatistician will choose the type of analysis after discussion with researcher. Note: For the above mentioned requirements, please provide hard copies as well, for items 1 and 3Describe CancerStemCellProject/ChangjiangXu/BiostatisticsService/DataRequirements here. |
* Animal strain (i.e. A/J mice) * Tissue/sample (i.e. lymphocytes) * Data type (i.e. gene expression data) * Chip used, along with version * Day/Date when the experiment was conducted, * If different samples were analyzed on different days, a list of which samples were analyzed on which days is needed. * The experimental layout of the study, i.e. which samples are located where on the chip results (tracking worksheet for the experiment) [if relevant] * Explanations for the column labels used in the raw data files * Copy of Tracking worksheet for your experiment 2. '''Raw data files''': standard format (comma delimited .csv format. In case of affymetrix .CEL files and CDF file to decode each .CEL file) * No comment fields in the data * Exactly one header line, naming all the columns using variable names that do not contain any spaces or underscores * A relevant set of row labels (e.g. probe_IDs) * Annotation file if your lab has prepared any special file 3. '''Description of the experiment’s goals''': clearly stated, including primary and secondary objectives, etc., proposed plan of analysis, if biologists have any particular technique in mind, and the biological rationale behind that choice. Otherwise the biostatistician will choose the type of analysis after discussing with researcher. Note: For the above mentioned requirements, please provide '''hard copies''' as well, for items 1 and 3. |
Data Requirements
Statistical data analysis for experiments in the Cancer Stem Cell Program is available by contacting Biostatistician Changjiang Xu at changjiang.xu@utoronto.ca. In order to ensure that appropriate analyses can be performed and all relevant information is provided, the following guidelines must be followed.
Required Laboratory Information: a complete and concise information about the experiment, including the following
- PI
- Researcher (student/postdoc) associated and contact information
- Technician
- Animal strain (i.e. A/J mice)
- Tissue/sample (i.e. lymphocytes)
- Data type (i.e. gene expression data)
- Chip used, along with version
- Day/Date when the experiment was conducted,
- If different samples were analyzed on different days, a list of which samples were analyzed on which days is needed.
- The experimental layout of the study, i.e. which samples are located where on the chip results (tracking worksheet for the experiment) [if relevant]
- Explanations for the column labels used in the raw data files
- Copy of Tracking worksheet for your experiment
Raw data files: standard format (comma delimited .csv format. In case of affymetrix .CEL files and CDF file to decode each .CEL file)
- No comment fields in the data
- Exactly one header line, naming all the columns using variable names that do not contain any spaces or underscores
- A relevant set of row labels (e.g. probe_IDs)
- Annotation file if your lab has prepared any special file
Description of the experiment’s goals: clearly stated, including primary and secondary objectives, etc., proposed plan of analysis, if biologists have any particular technique in mind, and the biological rationale behind that choice. Otherwise the biostatistician will choose the type of analysis after discussing with researcher.
Note: For the above mentioned requirements, please provide hard copies as well, for items 1 and 3.