1. 17 August 2012Ganesha Associates1 Basic reading, writing and informatics skills for biomedical research Segment 6. Experimental design

2. Introduction What is Experimental Design ? –Statistics? “The organization of an experiment to allow effective testing of the research hypothesis.” “The design of any information-gathering exercises where variation is present, whether under the full control of the experimenter or not.” 17 August 2012Ganesha Associates2

3. Some myths about ED Myth 1 –Its better to spend time collecting data than sitting around thinking about collecting data, just get into the lab/field and start making measurements! Reality –No! A well-designed experiment will save you a lot of time by eliminating unnecessary repetition and improving the precision of your measurements –Hint: analyse data as you generate it – quality control, test assumptions 17 August 2012Ganesha Associates3

4. Some myths about ED Myth 2 –“It doesn’t matter how you collect your data, there will always be a statistical ‘fix’ that will allow you to analyse them” Reality –No! Common problems are non- independence of data, lack of prior knowledge of the likely variance of parameters being measured, and absence of appropriate control or reference groups. 17 August 2012Ganesha Associates4

5. Some myths about ED Myth 3 –“If you collect lots of data something interesting will come out and you will be able to detect even very subtle effects” Reality –No! Generally collecting lots of data without a well-formulated hypothesis wastes your time and someone else’s money. –Remember that if you analyse a data set many different ways, you are bound to discover effects that have a p-value of less than 0.05. 17 August 2012Ganesha Associates5

6. 17 August 2012Ganesha Associates6 Start with the project proposal – quick check list Why is the problem under study of importance –Economic, medical significance ? –What are the underlying key issues of basic scientific significance –Establish strong links to the consensus view ? How is the problem to be addressed experimentally ? –Has an appropriate model system been chosen ? –What information needs to be collected ? –Which methods have been chosen for this purpose and why ? Limitations –Have the most-likely reasons for failure been identified ? –What is the ‘Fail early’ strategy ? Literature review –Is it up-to-date ? –Are all key points of logical development in the text backed by an appropriate reference ?

7. The anatomy of an experiment 17 August 2012Ganesha Associates7

8. The anatomy of an omics experiment A sample of cells (≈ obs units), from an organism (≈ exp units), with a history, on which the measurements are to be compared in one or more possible states, e.g. genotype, disease, chemical treatment (≈ treatments) to which a lot of delicate wet lab preliminaries - extraction, amplification, labelling are applied leading to the analyte being submitted to a complex piece of equipment, on which lots (10s - 1,000,000s) of measurements are made. 17 August 2012Ganesha Associates8

9. The anatomy of an omics experiment The measurements can be fluorescence intensities or counts, often highly pre-processed, with transformation, normalization and summarization usually being needed before analysis. There is rarely a single objective, and frequently no clearly stated goal; often it’s a screen ≈ fishing expedition, e.g. a good outcome can be finding ≥1, many, if not all genes or proteins or metabolites satisfying some condition. 17 August 2012Ganesha Associates9

10. Key factors to think about Baseline assumptions Sources of variance Need for technical, biological replication Sample size, statistical power and significance Choice of controls Non-independence of data Confounding variables Randomization, stratification Bias, blinding Multiple testing, data mining Inferring causality 17 August 2012Ganesha Associates10

11. 17 August 2012Ganesha Associates11 Collecting data – keep a notebook

12. 17 August 2012Ganesha Associates12 Collecting data – make a spreadsheet

13. 17 August 2012Ganesha Associates13 Collecting data – check key assumptions

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15. 17 August 2012Ganesha Associates15 Publication doesn’t guarantee that the design is correct!

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18. “Why Most Published Research Findings Are False” John Ioannidis, PLoS Medicine, 2005 Small studies are less likely the research findings are to be true. Small effect sizes are less likely to be true. The greater the number and the lesser the selection of tested relationships in a scientific field, the less likely the research findings are to be true. The greater the flexibility in designs, definitions, outcomes, and analytical modes in a scientific field, the less likely the research findings are to be true. The hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true. 17 August 2012Ganesha Associates18

19. 17 August 2012Ganesha Associates19 How citation distortions create unfounded authority Steven Greenberg, BMJ, 2009 Many published biomedical belief systems are built on sound data, with authors repeating claims after trusting the published expert opinion of their colleagues. However, there are incentives for generating and joining information cascades regardless of their soundness. Joining an information cascade aids publication as articles have to say something and negative results are biased against. Generating and joining an information cascade may improve the likelihood of obtaining research funding because hypothesis driven research is an essential requirement at many research funding agencies and successful funding generally requires a “strong hypothesis...

20. 17 August 2012Ganesha Associates20 In life sciences there are many unknowns “As we know, There are known knowns. There are things we know we know. We also know There are known unknowns. That is to say We know there are some things We do not know. But there are also unknown unknowns, The ones we don't know We don't know.” Donald Rumsfeldt, US Secretary of Defense (sic) Feb. 12, 2002, Department of Defense news briefing from "The Poetry of D.H. Rumsfeldt" http://slate.msn.com/id/2081042/

21. 17 August 2012Ganesha Associates21 Presenting your ideas Create a slide show that is an outline, not a script Use the slide show... –to select important information and visuals –to organize content –to create a hierarchy Many of the subsequent slides were adapted from work done by the Cain Project in Engineering & Professional Communication www.owlnet.rice.edu/~cainproj

22. 17 August 2012Ganesha Associates22 Selecting Content Consider your audience – not everyone will have your knowledge of the problem! State problem/question clearly, early and repeat (in the title, in the introduction) Explain the significance, context Include background: organism/system/model State the point of departure for work precisely

23. 17 August 2012Ganesha Associates23 Displaying Text Remember that your audience... –skims each slide –looks for critical points, not details –needs help reading/ seeing text –So keep to an outline only Help your audience by… –Projecting a clear font –Using bullets –Using content-specific headings –Using short phrases –Using grammatical parallelism

24. 17 August 2012Ganesha Associates24 Project a clear font Serif: easy to read in printed documents –Times New Roman, Palatino, Garamond Sans serif: easy to see projected across the room –Arial, Helvetica, Geneva

25. 17 August 2012Ganesha Associates25 Use bullets – but not too many Bullets help your audience –to skim the slide –to see relationships between information –organize information in a logical way For example, this is Main Point 1, which leads to... –Sub-point 1 Further subordinated point 1 Further subordinated point 2 –Sub-point 2

26. 17 August 2012Ganesha Associates26 Use content-specific headings “Results” suggests the content area for a slide “Substance X up-regulates gene Y” (with data shown below) shows the audience what is observed

27. 17 August 2012Ganesha Associates27 Use short phrases Be clear, concise, accurate Write complete sentences only in certain cases:  Hypothesis / problem statement  Quote  ??? Difficult to read DNA polymerase catalyzes elongation of DNA chains in the 5’ to 3’ direction Better DNA polymerase extends 5’ to 3’

28. 17 August 2012Ganesha Associates28 Use grammatical parallelism Use same grammatical form in lists Not Parallel: –Lyse cells in buffer –5 minute centrifuging of lysate –Supernatant is removed Parallel: –Lysed cells in buffer –Centrifuged lysate for 5 minutes –Removed supernatant

29. 17 August 2012Ganesha Associates29 Use grammatical parallelism How would you revise this list? Telomeres Contain non-coding DNA Telomerases can extend telomeres Cells enter senescence/apoptosis when telomeres are too short

30. 17 August 2012Ganesha Associates30 Use grammatical parallelism One possible revision… Telomeres Contain non-coding DNA Are extended by telomerase Cause senescence/apoptosis when shortened too much

31. 17 August 2012Ganesha Associates31 Displaying visuals Select visuals that enhance understanding –Figures from your work: evidence for argument –Figures from other sources (web; review articles): Model a process or concept Help explain background, context Design easy-to-read visuals –Are the visuals easy to read by all members of your audience? Draw attention to aspects of visuals

32. 17 August 2012Ganesha Associates32 Simplify and draw attention http://www.indstate.edu/thcme/mwking/tca-cycle.html

33. 17 August 2012Ganesha Associates33 Cite others’ visuals http://www.bioc.rice.edu/~shamoo/shamoolab.html Harvey et al. (2005) Cell 122:407-20

34. 17 August 2012Ganesha Associates34 Samples Features to consider: Text –Fonts, use of phrases, parallelism Visuals –Readability, drawing attention Slide design Organization/ hierarchy –Titles, bullets, arrangement of information, font size

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40. 17 August 2012Ganesha Associates40 The Calcium Ion Calcium is a crucial cell-signaling molecule –Calcium is toxic at high intracellular concentrations because of the phosphate- based system energy system –Intracellular concentrations of calcium are kept very low, which allows an influx of calcium to be a signal to alter transcription

41. 17 August 2012Ganesha Associates41 Microarrays Phillips G. (2004) Iowa State University College of Veterinary Medicine.

42. 17 August 2012Ganesha Associates42 Presenting Delivery Handling questions

43. 17 August 2012Ganesha Associates43 Delivery Physical Environment Stance –Body language –Handling notes Gestures Eye contact Voice quality –Volume –Inflection –Pace

44. 17 August 2012Ganesha Associates44 Handling Questions LISTEN Repeat or rephrase Watch body language Don’t pretend to know

45. 17 August 2012Ganesha Associates45 Practical activity 6a - Developing and presenting your project Total duration - ca. 2 hours. Identify the five most important research articles that frame your hypothesis, i.e. the fundamental facts and assumptions upon which your idea is based. Describe the basis for your hypothesis in a paragraph of no more than seven sentences. Read the article by Peter Norvig on experimental design. (For Firefox users the alternative URL is here.)experimental designhere. What alternative experimental approaches are available to answer your question ? How do you intend to verify your hypothesis? Identify and justify the journal you want to publish the results of your research in. Give a 5-slide presentation to justify your choices at the next session.

46. 17 August 2012Ganesha Associates46 Practical activity 6b - Thinking about probability and statistics Total duration - ca. 3 hours. First read the series of articles published recently by Wai-Ching Leung in the British Medical Journal. Although intended for a medical audience, these article provide the basis for a useful primer for all most fields of biomedical research. The articles are: Why and when do we need medical statistics Measuring chances Summarising information Testing hypotheses Now answer the following questions: I have a plant extract which I believe has an effect on blood pressure. I measure its effects by injecting the substance into rats and measuring their blood pressure before and after the injection. The statistical test I use tells me that the probability of collecting this sample of results is less than 0.05. What does this mean ? 1% of women aged forty who participate in routine mamography screening have breast cancer. 80% of the women with breast cancer get a positive result. 9.6% of women without breast cancer will also get a positive result. So, if a woman from this group gets a positive result, what is the probablity that she has breast cancer ? In the UK, car registration plates can typically consist of a string of 6 or 7 alphanumeric characters (A, B, C, etc, 1, 2, 3 etc). So the probability of a specific sequence of characters (e.g. DB1979) is less than 1 in 2 billion. I send a small group of people out into a car park and ask them to look for a registration plate that has personal significance for them. What is the likelihood of this happening ? A friend of mine has consistently predicted the results of 5 of the football matches leading to today's final. He is offering to sell me his prediction for the final match so that I can place a bet and make some money. What are the odds that he will predict the outcome of the last match correctly ? A murder is committed. Traces of your fingerprints are found on the murder weapon. What is the probability that you are guilty ?

47. 17 August 2012Ganesha Associates47 Practical activity 6c - Presenting data Total duration - ca. 1 hour. Read Mary Purugganan's presentation about data visualisation. Identify some examples of illustrations used in recent primary research papers which illustrate some of the points she makes.Mary Purugganan's presentation