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

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Statistical significance of bilayer biological network edges

I have a biological network with two types of nodes: genes and approved drugs. The edges can only exist between two different types of nodes. The mapping can be many-to-many (eg. a gene can be ...
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28 views

Best books for a population-ecology and biology statistics [closed]

I know that there is question that's similar to this (Books on statistical ecology?). I've got recommendations from that, but want to ask you for an advise following this list of books: 1. Applied ...
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10 views

How to find if any treatment is statistically better or worse in gene data given one standard method and 3 variations

Sorry I am a biologist and it appears am not quite confident enough for statistical analysis. I have datasets that represent different treatments on a biological system. It records how many genes have ...
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10 views

Comparing Peptide Amino Acid Composition: 2 Independent groups, Non-normal data, discrete data

I have two large groups of peptides, "positive" group (n = 368) and "negative" group (n = 880). The average length of the peptides (in each group) is about 20 amino acids. What I am trying to do is ...
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18 views

How to calculate F-measure with only Positive Data

I'm new in statistics and I have a question about finding f-measure once we do not have any "negative" data. I have a list of items with confidence score (between 0 and 1) calculated for each item: ...
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26 views

How can I calculate intraclass correlations for non-Gaussian over-dispersed data in R?

I have a dataset of behavioural measures from birds where each bird was measured twice over two days for five different behaviours. I would now like to see if the responses of individual birds are ...
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16 views

Paired studies: possible drawbacks

I have a question regarding paired studies. We are doing a medical study, we have a whole lot of data on a few hundred people and our aim is to study if a different level in one substance is linked to ...
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12 views

User weight specification in Meta-analysis using STATA

I want to perform Meta-analysis in STATA using User define weight option "wgt()", i.e., metan coef, fixed wgt(weight-variable). However, the model is not running, stata says, " too few variables ...
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1answer
65 views

What are the general methods for parameter estimation in statistics?

I have a task to estimate the probability of evolution selection of a given node. The only parameter estimation method I can think of is using the law of large numbers, i.e., use the proportion to ...
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67 views

Difficulty with logistic regression: logit transformation is non-linear

I am trying to perform a logistic regression to model likelihood of receiving a procedure given a certain diagnosis. There are several covariates to analyze but one of the main ones is patient age. As ...
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28 views

Nominal/Categorical Data Set

I have a nominal data set of a sample(species) floating characteristic(vertical floating, horizontal floating, bottom horizontal, and etc.) over a period of time. im interested to study the most ...
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15 views

Ttests for DNA sequences

Let's say I have two sets(1000 sequences in each set: set1 and set2) of independent DNA sequences of length 30. I created a HMM model by using DNA sequences in set1 which calculate Prob(Seq/Model). It ...
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10 views

State-space model: measurement-driven steps?

I have a time series that seems to be well described by a univariate local level model (a changing bias in human visual perception, sampled at regular intervals). I have a hunch, however, that the ...
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161 views

How to calculate the relative risk based on two independent confidence intervals

Medicine A cures 30% of patients (95% CI: 17 to 45). Medicine B cures 15% of patients (95% CI: 10 to 20). So I can divide 30% by 15% and say that medicine A is twice as likely to cure the patients ...
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31 views

Position Based statistics in DNA sequence

Let's say you have a DNA sequence with 21 positions, each of which can have one of four nucleotides (A,C,G,T). For example, If I see lot of C's and G's (called 'GC content') at 19th position in all ...
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12 views

Isolating distinct components of a treatment effect

The effect of a drug on blood analytes is to be studied. Blood analytes are measured before and after administration of the drug, which shows that several of them have decreased after treatment. A ...
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1answer
56 views

Doubt with a distance based Redundancy analysis

I conducted a distance based redundancy analysis (dbRDA) to explore the relevance of some environmental variables in explaining the patterns of the distribution (i.e., spatial and temporal) of two ...
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1answer
62 views

What type of test should i perform for my data?

I have a data frame with two columns. One for height and one for genotype. Genotype is a categorical variable consisting of 4 levels (B3, ein9, ein194, ein9xein194) and height is a numerical ...
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12 views

What does “ideal points” mean in multidimensional unfolding?

I am reading some materials about multidimensional unfolding and this concept "ideal points" are mentioned several times. I check these readings several times and could not find definition of this ...
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13 views

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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238 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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2answers
36 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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9 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
33 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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17 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
306 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
29 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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33 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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178 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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16 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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50 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
98 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
88 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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35 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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21 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
67 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
56 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
28 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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122 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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54 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
63 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
32 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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47 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
68 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
383 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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40 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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24 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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24 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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95 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 ...