Lecture notes for STIS students

1. Metodologi Penelitian
Komputasi Statistik
Setia Pramana

2. Educational Background
 Hasselt Universiteit, Belgium, MSc in Applied Statistics 2005-
2006.
 Hasselt Universiteit, Belgium, MSc in Biostatistics 2006-2007.
 Hasselt Universiteit, Belgium, PhD Statistical Bioinformatics,
2007-2011.

3. Educational Background
Medical Epidemiology And Biostatistics Dept. Karolinska
Institutet, Sweden, Postdoctoral, 2011-2014

4. Biostatistics
 The study of statistics as applied to biological areas
such as Biological laboratory experiments, medical
research (including clinical research), and public health
services research.
 Biostatistics, far from being an unrelated mathematical
science, is a discipline essential to modern medicine – a
pillar in its edifice’ (Journal of the American Medical
Association (1966)
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5. Bioinformatics
 Bioinformatics is a science straddling the domains of
biomedical, informatics, mathematics and statistics.
 Applying computational techniques to biology data
 Functional Genomics
 Proteomics
 Sequence Analysis
 Phylogenetic
 Etc,.
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6. “Informatics” in Bioinformatics
 Databases
 Building, Querying
 Object DB
 •Text String Comparison
 Text Search
 Finding Patterns
 AI / Machine Learning
 Clustering
 Data mining
 etc
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7. Current Research
 Statistical methods for high-throughput data analyses
particularly in Next generation sequencing (NGS) data
(Whole genome-seq, Exome-seq and RNA-seq).
 RNA microarray expression studies and GWAS in cancer
and cardiovascular diseases.
 Classification in NGS data.
 R-Graphical User Interface (R-GUI) for high-throughput
data analyses.

8. Course Outline
 Basic concept Research
 Problem identification and hypothesis
 Literature Review
 Research Design
 Quantitative research
 Make Scientific report/paper

9. Course Workload
 40% Theory, 60% practice
 Group Project (5 students)
 Presentation every week
 Slides can be seen at :
http://www.slideshare.net/hafidztio/
Setia Pramana Survival Data Analysis
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10. Research
 An organized, systematic, data-based, critical,
objective, scientific inquiry or investigation into a
specific problem, undertaken with the purpose of
finding answers or solutions to it.
 It provides the needed information that guides
managers to make informed decisions to successfully
deal with problems.
 The information provided could be the result of a
careful analysis of data gathered firsthand or of data
that are already available (in the company, industry,
archives, etc.).

11. Purpose of A Research
 Review or synthesize existing knowledge
 Investigate existing situations or problems
 Provide solutions to problems
 Explore and analyze more general issues
 Construct or create new procedures or systems
 Explain new phenomenon
 Generate new knowledge
 or a combination of any of the above!

12. Research Outcome
1. Product or Innovation directly used by Industry
2. Patent
3. International Publication

13. Types of Research, by Purpose
 Basic Research
 Applied Research
 Evaluation Research
 Research and Development

14. Types of Research, by Time
 Cross-Sectional Research
 Longitudinal Research

15. Types of Research, by Method
 Quantitative research:
 Descriptive
 Correlational research
 Causal-comparative
 Experimental
 Single-subject research
 Qualitative Research:
 Narrative research

16. Types of Research, by Method

17. Types of Research

18. Deductive Reasoning
 Starts out with a general statement, or hypothesis, and
examines the possibilities to reach a specific, logical
conclusion.
 The scientific method uses deduction to test hypotheses
and theories.
 Ex: "All men are mortal. Harold is a man. Therefore,
Harold is mortal."
Theory
Hypothesis
Observation
Confirmation

19. Inductive Reasoning
 The opposite of deductive reasoning.
 Makes broad generalizations from specific observations.
 Ex: "Harold is a grandfather. Harold is bald. Therefore,
all grandfathers are bald."
Theory
Tentative
Hypothesis
Pattern
Confirmation

20. Deductive/Inductive Research

21. Basic Steps
1. Develop a research question
2. Conduct thorough literature review
3. Re-define research question/ hypothesis
4. Design research methodology/study
5. Create research proposal

22. Basic Steps
6. Apply for funding
7. Apply for ethics approval
8. Collect and analyze data/Software
developing and testing
9. Draw conclusions and relate findings

23. Basic Steps

24. Research Question Development

25. Research Question Development
Problem Identification
Limit the research
scope
Research Question
Identification
Goals Identification
Hypothesis
Statistical Hypothesis
Hypothetical
Statement

26. Building block of Science

27. Possible Source of RQs
 Observational Research
 Discussions, brainstorming
 Experts, academics and industry
 Bibliography, journals, research report,
Populas science magazine, etc.

28. A Research Question Should
 Have research value: Original, can be
tested/evaluated.
 Fisible: Can be answered, data available,
cost and can be solved in time.
 Match to the researchers qualification

29. FINER criteria for RQ
 F Feasible Adequate number of subjects
 Adequate technical expertise
 Affordable in time and money
 Manageable in scope
 I Interesting Getting the answer intrigues
investigator, peers and community
 N Novel Confirms, refutes or extends previous
findings
Hulley S, Cummings S, Browner W, et al. Designing clinical research. 3rd ed.
Philadelphia (PA): Lippincott Williams and Wilkins; 2007.

30. FINER criteria for RQ
 E Ethical Amenable to a study that
institutional review board will approve
 R Relevant To scientific knowledge
 To clinical and health policy
 To future research
 Hulley S, Cummings S, Browner W, et al. Designing clinical
research. 3rd ed. Philadelphia (PA): Lippincott Williams and
Wilkins; 2007.

31. Research Hypothesis

32. Hypothesis Definition

33. Research Hypothesis
 The primary research question should be driven by the
hypothesis rather than the data.
 The research question and hypothesis should be
developed before the start of the study.
 A good hypothesis must be based on a good research
question at the start of a study and drive data collection
for the study.

34. Hypothesis
 Is a clear statement of what is intended to be
investigated.
 It should be specified before research is conducted and
openly stated in reporting the results.
 It allows to Identify:
 the research objectives
 the key abstract concepts involved in the research
 its relationship to both the problem statement and the
literature review

35. Source of Hypothesis
 Environment
 Literature
 Other Empirical Data
 Personal Experience

36. Type of Hypothesis
 Null Hypothesis
 Alternative Hypothesis

37. Type of Hypothesis

38. Example

39. Example
 There is no significant gain between pre-test and post-
test scored of students exposed to Computer-Aided
Instruction in Analytic Geometry

40. Special Consideration for Null
Hypothesis

42. Hypothesis Testing:

43.  1-sided or 2-sided hypotheses?
 A 2-sided hypothesis states that there is a difference
between the experimental group and the control group,
but it does not specify in advance the expected
direction of the difference.
 A 1-sided hypothesis states a specific direction (e.g.,
there is an improvement in outcomes with computer-
assisted surgery).
 A 2-sided hypothesis should be used unless there is a
good justification for using a 1-sided hypothesis.

44. Error Type

47. Research objective
 The primary objective should be coupled with the
hypothesis of the study.
 Study objectives define the specific aims of the study and
should be clearly stated in the introduction of the
research protocol.
 Example:
 Hypothesis : there is no difference in functional outcomes
between computer-assisted acetabular component placement
and free-hand placement,
 The primary objective can be stated as follows: this study will
compare the functional outcomes of computer-assisted
acetabular component insertion versus free-hand placement
in patients undergoing total hip arthroplasty.

48. Research objective
 The study objective is an active statement about
how the study is going to answer the specific
research question.
 Objectives state exactly which outcome measures
are going to be used within their statements.
 They are important to not only guide the
development of the protocol and design of study
but also play a role in sample size calculations and
determining the power of the study.

49. Literature Review

50. Literature Review
 Is an evaluative report of studies found in the
literature related to your selected area.
 Should describe, summarize, evaluate and
clarify this literature.
 Give a theoretical basis for the research and
help you determine the nature of your own
research.

51.  Select a limited number of works that are central
to your area rather than trying to collect a large
number of works that are not as closely connected
to your topic area.
Boote, D.N. & Beile, P. (2005). Scholars before
researchers: On the centrality of the dissertation
literature review in research preparation. Educational
Researcher 34/6, 3-15.

52. Literature Review Purpose
 Provide a context for the research
 Justify the research
 Ensure the research hasn't been done before
(or that it is not just a "replication study")
 Show where the research fits into the
existing body of knowledge
 Enable the researcher to learn from
previous theory on the subject

53. Literature Review Purpose
 Illustrate how the subject has been studied
previously
 Highlight flaws in previous research
 Outline gaps in previous research
 Show that the work is adding to the
understanding and knowledge of the field
 Help refine, refocus or even change the
topic

54. Strategies

55. Strategies

56.  Kirby, S., Greaves, L. & Reid, C. (2006). Searching the
Literature. In Experience research social change:
Methods beyond the mainstream

58. Literature Review in a thesis

59. The cycle
Hasibuan, 2007, Metode Penelitian Komputasi

60. What you should do
 Compare
 Contrast
 Criticize
 Synthesize
 Summarize
Hasibuan, 2007, Metode Penelitian
Komputasi

61. Sources
 Articles in International Journal
 Thesis
 Disertasi
 Proceeding
 Magazines
 Abstract book
 Websites

62. Literature Citation
 Whenever you quote, summarize, paraphrase or refer to
the work of another person you need to cite it.
 Giving credit to the original author for any information
that you learn through our research process and share
with the readers.
 Citing is the way to give credit to other's work when you
use it in your papers, speeches and projects.
 Citing other's work is a very important step in the
academic writing process and the best way to avoid
plagiarism.

63. Literature Citation
 Two ways:
 Use sentence that introduce the author
 Add the author’s name at the end of the sentence
 We must provide last name and year of publication
 Paraphrase signal phrase:
“According to Smith (2004) the cost of treating alcoholism is increasing
dramatically.”
 Direct Quote:
“ the cost of treating alcoholism is exceeded only by the cost of
treating illness from tobacco use, and is increasing exponentially”
(Smith, 2004)

64. Research Design

65. Research Design
 A plan or strategy for conducting the
research
 Spells out the basic strategies that
researchers adopt to develop evidence that
is accurate and interpretable.
 Deals with matters such as selecting
participants for the research and preparing
for data collection.

66. Purposes of Research Design
1. To provide answers to
research questions
2. To control variance

67. Purposes of Research Design
1. To provide answers to
research questions
2. To control variance

68. Characteristics for good research
design
1. Freedom from bias
2. Freedom from confusing
3. Control of extraneous
variables
4. Statistical correctness for
testing hypothesis

69. TYPES OF RESEARCH
1. Experimental research – involves
manipulating condition and studying
effects – (IPO-Input-Process-Output)
2. Correlational research – involves studying
relationship s among variables within a
single group, and frequently suggests the
possibility of cause and effect.
3. Survey research – involves describing the
characteristics of a group by means of
such instruments as interview schedules,
questionnaires, and tests.

70.  Ethnographic research - concentrates on documenting
or portraying the everyday experiences of people using
observation and interviews.
 Involve how well, how much, how efficiently,
knowledge, attitudes or opinion in the like exists.
 Case study – is a detailed analysis of one or a few
individuals
 Historical research – involves studying some aspect of
the past
 Action research – is a type of research by practitioners
designed to help improve their practice.

71. GENERAL RESEARCH TYPES
It is useful to consider the various
research methodologies we have
described as falling within one or
more general research categories –
Descriptive
Associational
Intervention-type Studies

72. 1. DESCRIPTIVE STUDIES
It describe a given state of affairs as fully and carefully
as possible.
Examples:
- In Biology, where each variety of plant and
animal species is meticulously described and
information is organized into useful taxonomic
categories.
- In educational research, the most common
descriptive methodology is the survey, as when
researchers summarize the characteristics
(abilities, preferences, behaviors, and so on) of
individuals or groups or physical environment
(school)

73. 2. ASSOCIATIONAL RESEARCH
 Research that investigates relationships is
often referred to as associational research
 Correlational and causal-comparative
methodologies are the principal examples
of associational research.
 Example: Studying relationship
(a) between achievement and attitude
(b) between childhood experiences and
adult characteristics

74. (c) between teacher characteristic and
student achievement
(d) between methods of instruction &
achievement (comparing students who
have been taught by each method)
(e) between gender and attitude
(comparing attitudes of males and females)

75.  Descriptive research is not satisfying since
most researchers want to have complete
understanding of people and things not just
merely describing but need further analysis.
 Associational studies are, they too are
ultimately unsatisfying.
- because it did not permit researchers to
“do something” to influence or change
outcomes.
- Simply determining interest or achievement
of students does not tell us how to change or
improve either interest or achievement.

76. 3. INTERVENTION STUDIES
 To find out whether one thing will have an
effect on something else, researchers need
to conduct some form of intervention
study.
 Is a particular treatment is expected to
influence one or more outcomes.
 Such studies enable researchers to assess

77.  For example:
- the effectiveness of various teaching
methods,
- curriculum models,
- classroom arrangements
- and other efforts to influence the
characteristics of individuals or groups.
 Experiment is the primary methodology
used in intervention research
 Some types of research may combine these
3 general types

78. Quantitative vs. qualitative research
Areas Quantitative Qualitative
Goals -Theory testing,
establishing
facts, statistical
description,
prediction,
relationship
between
variables
- Sensitizing
concepts,
describe
multiple
realities,
grounded
theory, develop
understanding
Design - Structured,
predetermined,
formal, specific
detailed plan of
operation
- Evolving,
flexible

79. Areas Quantitative Qualitative
Data -Quantitative,
quantifiable
coding counts,
measures,
operationalized
variables
statistics
- Descriptive,
personal
documents,
field notes,
photographs,
people’s own
words, official
documents
Sample - Large,
stratified,
control groups,
precise,
random, control
of extraneous
variables
- Small, non-
representative,
focused,
purposeful,
convenient

80. Areas Quantitative Qualitative
Technique or
methods
- Experiments,
surveys,
structured
interviewing,
structured
observation
- Observation,
participant
observation,
review of
documents,
open-ended
interviewing,
first person
accounts.
Relationship
with subjects
- Detached,
short term,
distant, subject-
researcher
restricted
- Empathy,
emphasis on
trust,
democratic

81. Areas Quantitative Qualitative
Data analysis - Deductive,
statistical
- Ongoing models, themes,
concepts, inductive,
analytic,constant
comparative.
Problems - Controlling
other
variables,
validity,
reliability
- Time consuming, data
reduction difficulties,
procedures not
standardized, difficulty to
study large
populations,Empathy,
emphasis on trust,
democratic

82. Research Types under Quantitative &
Qualitative
Quantitative Qualitative
1.Experimental
Research
2.Single-Subject
Research
3.Correlational
Research
4.Causal-Comparative
Research
5.Survey Research
1.Ethnographic
Research
2.Historical
Research

83. IDENTIFY WHAT TYPE OF RESEARCH
 Historical study of college entrance
requirements over time that examine the
relationship between those requirements
and achievement in mathematics.
 An ethnographic study that describes in
detail the daily activities of an inner-city
high school and also finds a relationship
between media attention and teacher
morale in school
 An investigation of the effects of different
teaching methods on concept learning and
gender

84. We can classify designs into a simple
threefold classification by asking some
key questions.

85. This threefold classification is especially useful for
describing the design with respect to internal validity.
A randomized experiment generally is the strongest of
the three designs when your interest is in establishing a
cause-effect relationship.
A non-experiment is generally the weakest in this
respect only to internal validity or causal assessment.
In fact, the simplest form of non-experiment is a one-
shot survey design that consists of nothing but a single
observation O.
The most common forms of research descriptive ones

86. What research type would be appropriate for
these research problem?
1. How do parents feel about the elementary school
counseling program?
2. Do students who have high score on reading tests also
have high scores on writing tests?
3. What effect does the gender of a counselor have on how
he or she is “received by counselees”?
4. How can Tom Adams be helped to learn to read?

87. ANSWER
 1. ETHNOGRAPHIC STUDY
 2. CORRELATIONAL STUDY
 3. CAUSAL-CORRELATION STUDY/INTERVENTION STUDY
 4. EXPERIMENT/CORRELATIONAL OR
ASSOCIATIONAL-INTERVENTION STUDY

89. Sampling Methods

90. What exactly IS a “sample”?

91. What exactly IS a “sample”?
A subset of the population, selected
by either “probability” or “non-
probability” methods. If you have a
“probability sample” you simply
know the likelihood of any member
of the population being included (not
necessarily that it is “random.”

92. SAMPLING
9
3
 A sample is “a smaller (but hopefully
representative) collection of units from a
population used to determine truths about that
population” (Field, 2005)
 Why sample?
 Resources (time, money) and workload
 Gives results with known accuracy that can be
calculated mathematically
 The sampling frame is the list from which the
potential respondents are drawn
 Registrar’s office
 Class rosters
 Must assess sampling frame errors

93. SAMPLING…….
94
 3 factors that influence sample representative-
ness
 Sampling procedure
 Sample size
 Participation (response)
 When might you sample the entire population?
 When your population is very small
 When you have extensive resources
 When you don’t expect a very high response

94. Assumptions of quantitative
sampling
We want to generalize to the
population.
Random events are
predictable.
Therefore…We can compare random
events to our results.
Probability sampling is the
best approach.

95. 96
SAMPLING BREAKDOWN

96. SAMPLING…….
97
TARGET POPULATION
STUDY POPULATION
SAMPLE

97. Process
98
 The sampling process comprises several stages:
 Defining the population of concern
 Specifying a sampling frame, a set of items or
events possible to measure
 Specifying a sampling method for selecting
items or events from the frame
 Determining the sample size
 Implementing the sampling plan
 Sampling and data collecting
 Reviewing the sampling process

98. Assumptions of qualitative
sampling
Social actors are not
predictable like objects.
Randomized events are
irrelevant to social life.
Probability sampling is
expensive and inefficient.
Therefore…
Non-probability sampling is
the best approach.

99. Types of samples

100. Types of Samples 101
 Probability (Random) Samples
 Simple random sample
 Systematic random sample
 Stratified random sample
 Multistage sample
 Multiphase sample
 Cluster sample
 Non-Probability Samples
 Convenience sample
 Purposive sample
 Quota

101. Simple Random Sample
1. Get a list or “sampling frame”
a. This is the hard part! It must not systematically exclude
anyone.
b. Remember the famous sampling mistake?
2. Generate random numbers
3. Select one person per random number

102. SIMPLE RANDOM SAMPLING……..
103
 Estimates are easy to calculate.
 Simple random sampling is always an EPS design, but not all
EPS designs are simple random sampling.
 Disadvantages
 If sampling frame large, this method impracticable.
 Minority subgroups of interest in population may not be
present in sample in sufficient numbers for study.

103. Systematic Random Sample
1. Select a random number, which will be known as k
2. Get a list of people, or observe a flow of people (e.g.,
pedestrians on a corner)
3. Select every kth person
a. Careful that there is no systematic rhythm to the flow
or list of people.
b. If every 4th person on the list is, say, “rich” or “senior”
or some other consistent pattern, avoid this method

104. SYSTEMATIC SAMPLING……
105
 ADVANTAGES:
 Sample easy to select
 Suitable sampling frame can be identified easily
 Sample evenly spread over entire reference population
 DISADVANTAGES:
 Sample may be biased if hidden periodicity in population
coincides with that of selection.
 Difficult to assess precision of estimate from one survey.

105. Stratified Random Sample
1. Separate your population into groups or “strata”
2. Do either a simple random sample or systematic
random sample from there
a. Note you must know easily what the “strata” are before
attempting this
b. If your sampling frame is sorted by, say, school district,
then you’re able to use this method

106. STRATIFIED SAMPLING……
107
 Drawbacks to using stratified sampling.
 First, sampling frame of entire population has to be
prepared separately for each stratum
 Second, when examining multiple criteria, stratifying
variables may be related to some, but not to others,
further complicating the design, and potentially reducing
the utility of the strata.
 Finally, in some cases (such as designs with a large number
of strata, or those with a specified minimum sample size
per group), stratified sampling can potentially require a
larger sample than would other methods

107. Multi-stage Cluster Sample
1. Get a list of “clusters,” e.g., branches of a company
2. Randomly sample clusters from that list
3. Have a list of, say, 10 branches
4. Randomly sample people within those branches
a. This method is complex and expensive!

108. The Convenience Sample
1. Find some people that are easy to find

109. The Snowball Sample
1. Find a few people that are relevant to your topic.
2. Ask them to refer you to more of them.

110. The Quota Sample
1. Determine what the population looks like in terms of
specific qualities.
2. Create “quotas” based on those qualities.
3. Select people for each quota.

111. The Theoretical Sample

113. Jenis Penelitian untuk Skripsi
Komputasi Statistik STIS
 Pengembangan sistem informasi statistik
Sistem informasi berbasis komputer yang dikembangkan
untuk mendukung kegiatan pada domain/area statistik.
Contoh: Sistem Informasi Rujukan Statistik, Sistem
Informasi Geografis yang menggunakan data (hasil olahan)
statistik, Sistem Informasi Diseminasi Statistik, serta
Sistem Informasi Data Entri dan Monitoring dalam kegiatan
pengumpulan data statistik.

114. Jenis Penelitian untuk Skripsi
Komputasi Statistik STIS
 Pengembangan aplikasi statistik
Program aplikasi yang dibuat untuk mendukung pemecahan
masalah di bidang statistika.
Program harus dibuat sendiri dan pemecahan masalah tersebut
belum bisa dilakukan dengan menggunakan paket program
pengolahan data statistik yang sudah ada; atau program boleh
dibuat dengan menggunakan pustaka/library yang sudah ada
namun belum ada interface nya; atau bisa dilakukan dengan
paket program namun proses/prosedurnya tidak/belum efisien
sehingga perlu dibuat suatu aplikasi yang terintegrasi.
Contoh: Pengembangan Aplikasi Fitting Regresi, Aplikasi
Pengujian Hipotesis Menggunakan Permutation Test dalam
Resampling.

115. Jenis Penelitian untuk Skripsi
Komputasi Statistik STIS
 Kajian teknologi di bidang komputasi statistik
Kajian yang dilakukan pada dua bidang keilmuan tersebut yang
hasilnya dapat bermanfaat bagi perkembangan ilmu komputer
maupun statistik.
Tema penelitian yang tidak masuk dalam jenis pertama dan kedua
bisa dimasukkan ke dalam jenis ketiga ini jika dipandang tema
penelitiannya memiliki orisinalitas dan inovasi serta tingkat
kontribusi yang tinggi bagi perkembangan ilmu komputer maupun
statistik, Badan Pusat Statistik, maupun bagi masyarakat.
Contoh: Pengembangan Inference Engine Sistem Pakar Berbasis
Database (Studi Kasus Penentuan Metode Penyusunan Indeks Harga
dan Produksi), Pengembangan Mesin Pencari Statistik Berbasiskan
Supervised Learning dan Relevant Feedback.

116. Metode,Teknik Dan Instrumen
Dalam Penelitian
 Research Instruments:
 Tools for gathering data
 Questioners
 Interview

117. Questioners
 The most common instrument or tool of research for
obtaining the data beyond the physical reach of the
observer which
 Closed form / Closed-ended
 Open form / Open-ended

118. Questioners
 Clarity of language
 Singleness of purpose
 Relevant to the objective of the study
 Correct grammar

119. Questioner: Advantages
 Facilitates data gathering
 Is easy to test data for reliability and validity
 Is less time-consuming than interview and
observation
 Preserves the anonymity and confidentiality of the
respondents’ reactions and answers

120. Questioner: Disadvantages
 Printing and mailing are costly
 Response rate maybe low
 Respondents may provide only socially acceptable
answers
 There is less chance to clarify ambiguous answer
 Respondents must be literate and with no physical
handicaps
 Rate of retrieval can be low because retrieval itself is
difficult

121. Interview
Purpose:
 to verify information gathered from written sources
 to clarify points of information
 to update information and
 to collect data

122. Interview: Types
 Screening interview
 Panel or Group Interview
 Telephone interview

123. How to measure the instruments?
 Validity- measure what is intends to measure
 External validity: is the results of a study can be generalized from a
sample to a population?
 Content validity: The appropriateness of the content of an
instrument. In other words, do the measures (questions, observation
logs, etc.) accurately assess what you want to know
 Reliability – stability in maintaining consistent measurement in
a test administered twice
 Inter-Rater/Observer Reliability: The degree to which different
raters/observers give consistent answers or estimates.
 Test-Retest Reliability: The consistency of a measure evaluated over
time.
 Parallel-Forms Reliability: The reliability of two tests constructed the
same way, from the same content.
 Internal Consistency Reliability: The consistency of results across
items, often measured with Cronbach’s Alpha.