The science of statistics applied to the analysis of biological or medical data.

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Power analysis for environmental microbiology samples

In my experiment, I will be taking environmental samples in cheesemaking rooms of 20 dairy farms (each sampling point is a 10cm x 10cm square area that I swab and count the microorganisms I found back ...
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1answer
38 views

How to interpret $\delta$ in the analysis of this article?

Goal I ran some population genetics numerical simulations where an effect of interest is observed whenever there is a tendency of individuals to migrate more toward one direction than toward the ...
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1answer
145 views

Good examples of statistics sections in applied academic journal articles

I am a biostatistician working in an applied field and I am responsible for writing the statistics methods section for the papers I collaborate on. In reading a lot of academic papers I've come ...
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7 views

Indicator species analysis in R (labdsv package) [migrated]

I am trying to do indicator species analysis in R using the labdsv package. I was able to get it to work on previous sequencing data set but now it has thrown ...
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2answers
25 views

Statistical test to compare paired scores

I would like to measure (to quantify with a statistical test) how much different are paired scores. For example: for gene "x" I performed an experiment with technology A that gives a score, then for ...
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6 views

How to analyse interbirth interval data with 0s

OK.. So to give a bit of context, this is what my data looks like: My question is regarding the last variable column (IBI). This records the interbirth interval in days between each birth (the date ...
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1answer
21 views

Coefficient of variation for a subset

How do I calculate the coefficient of variation, CV (or Relative Standard Deviation, RSD) for a subset? e.g. ...
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0answers
14 views

Permuted block design Wilcoxon sum rank test

I need to do a Wilcoxon rank sum statistic for some data with a permuted-block with 2 blocks of size 6. However, I'm confused how we deal with the permuted-block randomization. My book says When ...
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1answer
298 views

What does a random walk do exactly?

To be honest, I have read many websites and answers regarding to this question, and none explained it in simple words which are understandable. What I want to do is to understand what a random walk ...
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1answer
25 views

Probability of a deleterious mutation, given an observed distribution of mutations

This problem has been driving me crazy for days, so I finally resort to asking for help here: Consider a set of genes, where each gene consists of a sequence of letters, for example ...
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22 views

compute the ratio of odds ratios and its confidence interval

How would one compute the ratio of odds ratios and its confidence interval? for example: OR1=1.07; ci=0.88-1.29 OR2=1.27; ci=0.78-1.39
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2answers
168 views

Reconstruction of Species Distribution based on poorly-sampled data

cross-posted to Signal Processing, World Building, and Biology Stack Exchange Problem: After reading a series of fantasy novels, I noticed that the biosphere in that world made no sense. To clarify, ...
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9 views

Cronbach's alpha

I want to use the EAT-26 in my study , and the zero frequency is high in scoring because more than one answer represent zero in scoring ( never=0,rarely=0,sometimes=0) , so Cronbach's alpha is low ?! ...
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26 views

Kruskal-Wallis post hoc comparisons different results in different software used

I'm having some trouble analyzing my data because when I use StatSoft Statistica and run a Kruskal-Wallis, I get one set of values for multiple comparisons, but when the same analysis is run in XLSTAT ...
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2answers
77 views

Help performing hypothesis tests automatically on a large data set in R

I have a data frame in R with 100 variables (columns) and 100 observations (rows). Each row is a patient; the columns are different variables such as gender, height, body-mass index, etc. I know that ...
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1answer
85 views

How do you tell if you should use a one-tailed test or a two-tailed test in a t-test?

For example, how would you decide between which tailed test to do in the following experiment: Ethanol dilutions were made with different proportions and Daphnias were submerged in them to collect ...
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18 views

Statistical analysis of time to event data

If I have 2 events of interest, lets say $X$ and $Y$. I would like to know, what is the influence of $Y$ on $X$. It's like a correlation between 2 events, but I'm not sure what is the formal test for ...
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1answer
20 views

jackknifing blocks (*not* time series)

I have the following problem. There are 50 subjects. Each subject does a block of 100 trials. At the end I want to compute a complicated statistic s() on the data x. Now I want to be able to compute ...
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2answers
54 views

Biostatistics book for mathematician

It would be great if you could recommend me some books on biostatistics for people with a solid background in mathematics. I have an MSc in mathematics and a PhD in bioinformatics/machine learning, ...
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1answer
33 views

Are sensitivity and specificity complement of each other?

Sensitivity : probability that a person with the condition will be classified in one's study as having the condition. ...
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1answer
24 views

Why is screening test more concerned about sensitivity while diagnostic test is more concerned about specificity?

Screening Test : A large number of apparently healthy people are tested to identify those who are at a risk of the condition or disease. ...
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1answer
107 views

DNA exoneration: what are the chances?

As with any biometric, both the False Acceptance Rate (i.e. what is the chance that two samples of different individuals match) as well as the False Rejection Rate (i.e. what is the chance that two ...
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47 views

How can I use the posterior distribution of parameters from one model in another model?

I would like to model different effects of siRNA treatment on measurements. Cells are grown in 384-well plates, subjected to different siRNA treatment and then imaged to determine parameters. Around ...
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1answer
58 views

calculation of variance

Hi I have a question regarding calculation of variance of survey results. Consider the following example. If 5 (x) people answered a survey which consists of 3 (y) yes (1) or no (2) questions. You ...
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1answer
30 views

Controlled clinical trial, what is controlled refering to?

We say a (randomized) controlled clinical trial for a specific study design. Now my question is, what is controlled refering to? Different things come up to my mind: Controlled in the sense that ...
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0answers
36 views

How did they do this analysis? (weighted proportions)

I've read with interest the report by Ayanian et al "Racial and Ethnic Disparities among Enrollees in Medicare Advantage Plans" [1]. They have estimated adjusted proportions of individuals that ...
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1answer
55 views

What is a Dirichlet prior

I am doing some bioinformatics research but my background is Applied Math and I usually have trouble with the statistics part of it. Basically, I've created a Position Weight Matrix using a R ...
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1answer
202 views

What are hot research topics for PhD dissertation in Biostatistics?

I've been thinking of choosing research topics for PhD dissertation in Biostatistics. I wish to know some hot research topics in recent years. As far as I know, some hot research topics are: ...
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1answer
54 views

Find distribution of underlying feature

Let's say I have a dataset with values for the variable $W$. The distribution of $W$ doesn't follow any obvious known distribution. I have a model that gives $W$ as a functions of $E$ and $K, W = ...
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36 views

nested multilevel model for differential expression analysis

I have read several other postings regarding nested models, but they did not seem to exactly capture my particular case, and I'm a bit unsure how to proceed with analysis of my model. Any help would ...
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21 views

Can Anyone explain the significance of Q-mean value?

I have been using the Swiss Model for modelling protein structures. It returns the modelling result with the estimation of nativeness of the structure through the Q-mean4 value. I have even read the ...
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23 views

Separation of Two Sub-populations

Background: I have a large table with 7683 rows and 42 columns containing features of cells (endothelial cells), relating to their morphometric characteristics, for example the cell area, the longest ...
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1answer
78 views

Post-hoc after GLM: What does it exactly say?

Background: I have been asked to model the change of weight of a few animals undergoing experimentation via a simple GLM (General Linear Model). The data looks something like this. Note that all data ...
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36 views

Difference in Difference

How to interpret parameter of difference in difference with respect to public health ? Students had taken special care from 2010(baseline) to 2011(follow-up)period. say, in regression approach ...
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0answers
14 views

Modeling Switch-Like vs Continuous Signal

I'm currently trying to figure out the best way to model a given scenario, but am unsure of the best way to go about it, so I'll explain the situation in as much detail as possible. So I work in a ...
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14 views

selecting genes specific/agnostic to condition

I have a microarray transcriptomics experiment. The design of which is something like this : ...
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2answers
114 views

Machine Learning and Biostatistics [closed]

I am interested in a few areas with biostatistics, and was reading the course catalog at a university that offers machine learning. I am taking topology now, and i think machine learning uses ...
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1answer
225 views

Test(s) For Comparing qPCR results / ΔΔCт values

To be clear, I'm talking about real-time polmerase chain reaction (qPCR), not Principle Component Regression. Though from a company selling qPCR reagents, here is a good walk-through of the ...
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25 views

What books to read for Biostatistician position supporting product develpment for in -vitro diagnostics?

This is not a question concerning a specific statistical method, but I need an advice. I am interested in a position as a biostatistician to support product development for in-vitro diagnostics. I ...
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31 views

Testing of sensitivity for different algorithms

I have some queries I would like to discuss, I am doing some analysis for sensitivity. I am not from the field of statistics. I work with RNA-Seq data. The thing is I have found some genes which are ...
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1answer
39 views

Controlling random deviation in a birth-death process

I have a process in which $X$ is a molecule going through birth ($x \rightarrow x + 1$) and death $(x \rightarrow x - 1)$. Rate of both reactions, namely synthesis rate for birth and elimination rate ...
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1answer
99 views

Bayesian inference of a clinical trial for clinicians

I am a clinician who is more adept than average at interpreting clinical trials in a frequentist manner. At this point, interpreting a trial as a frequentist has kind of become a procedure: check ...
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14 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook [Probability Models for DNA Sequence Evolution][1] by Durrett. In chapter 1, he discusses the Wright ...
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3answers
135 views

Beyond the basics: intermediate medical statistics textbooks suggestions

I am a soon-to-be physician. During my studies I have taken a class in biostatistics. I own Martin Bland's "An introduction to medical statistics", which was a required textbooks at the time, and ...
2
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1answer
38 views

wilcox.test usage in R

I would like to know if there is a difference in the values taken from measurements of a given characteristic sampled at primary forest (Point=1) and secondary ...
4
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1answer
119 views

Does an exponential model fit my data?

I am measuring accumulation of a fluorescent-tagged protein at a particular location within a cell over time. In previous experiments that I have performed, I see a standard exponential distribution ...
4
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1answer
107 views

Identifying the experimental unit

I have included a diagram of an experiment where cells are pooled from multiple animals, cells from the pool are then allocated to different treatments and a measurement is taken from each individual ...
2
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1answer
1k views

Standard Deviation After Subtracting One Mean From Another

I've got two sets of data from some fluorescent cells. The first set is when the cells don't have their fluorescence switched on, but they are still faintly glowing. The second set is when they do ...
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2answers
26 views

Interaction between variables

I would like to regress basal metabolic rate (BMR) on height, weight, age and gender. How do I do this taking into consideration the interaction between the variable? Wouldn't I have to consider ...
2
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2answers
104 views

Best distribution to handle a ratio of counts as a response variable

A quick statistics question (apologies for the added biology): I have two sets of counts (for the expression of two different isoforms of a particular gene), and to generate the response variable in ...