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Statistics January - March 2011 Tim Bunnell, Ph.D., Jobayer Hossain, Ph.D., Larry Holmes, Ph.D. Nemours Bioinformatics Core Facility Nemours Biomedical Research Overview • Class goals – Master basic statistical concepts – Learn analytic techniques & when to apply them – Learn how to interpret analysis results – Develop familiarity with SPSS & REDCap – Gain understanding that will transfer to a broad range of other statistics tool Nemours Biomedical Research Overview • Class structure – 8 sessions – 1.5 hours per session – Several homework assignments • Class website – http://www.nemoursresearch.org/open/StatClass/January2011 Nemours Biomedical Research Statistics Science of collection, presentation, analysis, and reasonable interpretation of data. Nemours Biomedical Research Types of Data or Variables • Variable - any characteristic of an individual or entity. – A variable can take different values for different individuals. – Variables can be categorical or quantitative. Per S. S. Stevens… • Types – Nominal - Categorical variables with no inherent order or ranking sequence such as names or classes (e.g., gender). Value may be a numerical, but without numerical value (e.g., I, II, III). The only operation that can be applied to Nominal variables is enumeration. – Ordinal - Variables with an inherent rank or order, e.g. mild, moderate, severe. Can be compared for equality, or greater or less, but not how much greater or less. – Interval - Values of the variable are ordered as in Ordinal, and additionally, differences between values are meaningful, however, the scale is not absolutely anchored. Calendar dates and temperatures on the Fahrenheit scale are examples. Addition and subtraction, but not multiplication and division are meaningful operations. – Ratio - Variables with all properties of Interval plus an absolute, non-arbitrary zero point, e.g. age, weight, temperature (Kelvin). Addition, subtraction, multiplication, and division are all meaningful operations. Nemours Biomedical Research Descriptive & Inferential Statistics • Descriptive Statistics: Summarizing or characterizing data – What is the mean, standard deviation, or distribution (for quantitative variables such as age, height, or weight). – What are the counts, relative frequency, or percentages (for categorical variables such as gender, eye color, or disease status). • Inferential Statistics: Drawing conclusions from the immediate data; predicting. – What is the probability that these two groups of subjects were sampled from the same population? – What is the likelihood this child has disease X given the results of an assay? – How large a dose is needed to achieve a specific response level? Nemours Biomedical Research Population and Sample • Population: The entire collection of individuals or measurements about which information is desired. • Sample: A subset of the population selected for study. – Primary objective is to create a subset of population whose center, spread and shape are as close as possible to that of population. Nemours Biomedical Research Parameter v.s. Statistic • Parameter: – Any statistical characteristic of a population. – E.g., population mean, median, standard deviation are parameters. – Parameters describe the properties of a population – Parameters are usually unknown – Parameters are fixed unless the population changes. Nemours Biomedical Research Parameter v.s. Statistic • Statistic: – A characteristic of a sample drawn from a population. – E.g., sample mean, median, standard deviation are statistics. – Statistics estimate properties (parameters) of a population – Statistics are known exactly (because calculated) – Statistics usually vary from one sample to another. – Are used for making inferences about parameters Nemours Biomedical Research Statistical Inference sample population • Statistical inference is the process by which we acquire information about populations from samples. • Two types of estimates for making inferences: – Point estimation. – Interval estimate. Nemours Biomedical Research Statistics Science of collection, presentation, analysis, and reasonable interpretation of data. Science of collection, management, presentation, analysis, and reasonable interpretation of data. Nemours Biomedical Research REDCap • REDCap (Research Electronic Data Capture) • A secure, web-based application for building databases and collecting and managing data • Users can create and design their own databases, enter their data as it is collected and export data formatted for import into common statistical packages (i.e. SPSS, SAS, STATA and R) • A calendar function allows scheduling of events and appointments. Nemours Biomedical Research REDCap • Initially developed and deployed at Vandervilt University • Now supported by a consortium of a growing number of partner institutions • Citation: Harris PA, Taylor R, Thielke R, Payne J, Gonzalez N, Conde JG. Research electronic data capture (REDCap)--a metadatadriven methodology and workflow process for providing translational research informatics support. J Biomed Inform. 42 (2):377-81, 2009. Nemours Biomedical Research Why use REDCap? • Accessibility – Everyone working on the project can get to the data – Data entry can be done from anywhere • Security – Data is stored on our servers, backed up nightly – Users must authenticate to view the data – Users can be assigned different levels of permission such as read-only, add/edit data, delete records, etc – Users can be restricted from viewing certain forms and exporting certain fields Nemours Biomedical Research Why use REDCap? • Versatility – Data or data subsets can be easily selected, sorted and exported in formats directly ready for analysis in SPSS, SAS, S+/R or even Excel – Schedules can be automatically generated from defined events • Validity – Using a tool like REDCap to set up a database and data entry forms for a study is a valuable first step in being sure that you have covered all the devilish details that are inherent in designing a valid research study Nemours Biomedical Research REDCap Training • Training Videos – REDCap overview (watch this before the next session) – Other REDCap basics – Types of REDCap databases – Special features • Website https://www.nemoursresearch.org/redcap /index.php?action=training Nemours Biomedical Research REDCap Accounts • Accounts – Every REDCap users is assigned a unique account – Passwords should be kept confidential. Do not share your password with anyone else – Only sign on and use the system under your own username and password – Always log off the system before leaving the site. – You will each receive an email message with your REDCap username and password – There will be two databases that contain data sets for the class Nemours Biomedical Research Statistical Tools & Packages • Excel – – • SAS – – – • More academic background than SAS Still quite powerful and less expensive R – – – – • Other extreme from Excel Industrial-strength statistics Programming language + functions STATA – – • Rudimentary data summarization and analysis. It’s everywhere Freely available, open source statistical programming environment Excellent graphics capabilities Extensive library of functions and packages with online support community Ghastly learning curve! SPSS – – – Statistical Package for the Social Sciences Grown into a well-supported and fairly user friendly package Our tool of choice for user-generated statistical analyses in Nemours Nemours Biomedical Research SPSS • Available from Citrix Metaframe Server – External connection via Connect2 – Internal use Metaframe desktop link • Everyone has permission to use it • Limit of 17 licenses total for all Nemours • Limit of 10 licenses for this class Nemours Biomedical Research