The science of statistics applied to the analysis of biological or medical data.
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11 views
Antisense Transcript Level
The basic biology says genes on the DNA, get transcribed to mRNA (sense transcription), and the RNA will be translated to proteins. but sometimes, a gene can have transcription from the opposite ...
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15 views
What role(s) does Statistical Computing / Computational Statistics play in Clinical Trials?
I am going to pursue a PhD in Statistics, and the two fields that I am really interested are Statistical Computing / Computational Statistics and Clinical Trials (mainly because I like doing ...
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29 views
Standard Error of the ratio of multinomial and negative binomial variables
What is the correct way to compute a standard error of the ratio between random variables following multinomial and negative binomial distribution?
I asked a question about computing variance in the ...
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1answer
25 views
Estimation of partitioning error in next-generation sequencing experiments
[Edited: explanation of the partitioning error]
I would like to estimate how the initial number of molecules (or the level of gene expression) affects reproducibility between technical replicates of ...
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8 views
How do I know the margin of error of my predicted values?
Questions will be written using bold formatting:
I have come up with a model on R that gave me the following output:
I've been asked to create a confusion matrix in order to compare my predicted ...
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15 views
How to test null hypothesis of “observer A sights animal at the same time that observer B sights animal”
I have 2 observers at different platforms making sightings of animals in the wild. Observers work independently of one another. Observers record when an animal was sighted, as well as the location of ...
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29 views
Analyzing Pre/Post Binary Outcomes - What type of model is appropriate?
I apologize for the rudimentary questions. This was not my study, and I am only tasked with analyzing the data.
Background
I am analyzing data on awareness of tobacco health risks before and after an ...
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1answer
22 views
Difference between log normal probability density values
just reviewing two resources, I noticed a difference between the log normal p.d values :
One is here
which takes the e to the power in which it contains ln(x)
the other is here
Which on page 5 , ...
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21 views
Writing syntax for bivariate survival censored data to fit copula models in R
Am required to fit copula models in R for different copula classes particulary the
Gaussian, FGM,Pluckett and possibly Frank (if i still have time). The data am using is Diabete data available in R ...
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1answer
71 views
What statistical tests should I use on my data?
My project is on the behavioural responses of anemonefish to a camera flash at different depths.
I only had two weeks and no internet to collect my data, please don't judge me too hard!
My ...
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2answers
31 views
Terminology for 'prevalence' when it's number of people and not a proportion?
'Prevalence' is usually used to describe a proportion or rate, e.g. '5% $\pm$ 2% of the population are Blue'. What do you call this when you estimate the actual number of people in a population with a ...
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1answer
19 views
How to calculate correlation of 2 variables combined
I have data on 2 histone marks that influence chromatin density. I have calculated individual correlation scores using the cor.test() function in R for both. I would like to combine the 2 together to ...
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1answer
69 views
Why are PhD programs in statistics coursework heavy relative to PhD programs in the basic sciences?
This might go better on academia stack exchange, but it seems probably the people who know the answer are on cross validated..
This is a pattern across the US. My classmates in, e.g., neuroscience ...
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1answer
26 views
Difference between NA and None in biological dataset
I have collected environmental data on animals, and am seeking help on how to deal with certain variables where a non-numeric value is informative, but also problematic. I have three variables that ...
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28 views
Test distribution normality from grouped data in R
So, there is the question: is there any statistical methods exist to apply normality test (hypotesis check) for grouped data?
For example, take a look at data frame:
...
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2answers
29 views
Best statistical test to compare proportions of count data
I have taken photos of 30 animals moving around an arena. The arena has 4 different configurations, and I have 500 photos for each animal in each type of arena (taken throughout the day). I have gone ...
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1answer
36 views
multgee for repeated measure multinomial regression
I am trying to analize my experiment results according to the multgee reference pdf, but I have some warning message.
My dependent variable is a 5 level categorical variable. I have 12 eyes of 6 rat,...
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1answer
67 views
Biological and technical replicates - mixed model?
I'm trying to make sure I use the correct statistical tests on a group of experiments. Suppose I perform 5 experiments. In each experiment a single batch of cells is partitioned into 6 batches of ...
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1answer
26 views
Statistical test for differences between proportions, with many zeroes
I have collected data in the form of percentages, ie. what % of the population has Trait A? I measured the frequency three times for each population, giving three replicates. My ultimate goal is to ...
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1answer
42 views
Deep learning in medicine(Articles)
I am looking for the articles in Medicine, where deep learning techniques were applied. I googled but I found only tutorials.
Maybe you can provide me good articles?
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22 views
What statistical test would be best for before and after comparisons of multiple similar groups?
I can't exactly give the problem I'm working on but I will give a sensible example of how it looks:
I have 4 groups of people: diabetes, depression, schizophrenia, dementia, notice how a person with ...
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109 views
Correcting for noise in gene expression data
I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a logistic regression classifier.
I also ...
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0answers
31 views
Does the absolute values of the %IncMSE in Random Forest hint at predictive power of a variable?
I am new to machine learning. I am researching the drivers of plant species richness in woodlands. I have the species richness and a set of predictors, eg, pH, soil organic matter etc for around 100 ...
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13 views
How to fit a distribution to a function of binned values
I am interested in fitting power law or Pareto distributions to a set of values. First, we assume that the abundance $A$ of an organism is related to mass $M$ with a power law with exponent -2: $A \...
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25 views
Batch effects in survival data
I have a problem concerning batch effects in survival data of C.elegans.
I read through a few forum posts and a paper but I am still not really getting it.
In the experiment the effect of different ...
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24 views
Predicting the probability of diabetes
I have collected comments of diabetes patients. In these comments they have also mentioned other symptoms.
Now patients come to my portal to check diabetes possibilities. User enters x,y,z symptoms. ...
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How to work out degree exponent for protein-protein interaction networks (cyctoscape, NetworkAnalyzer)?
I’m working with a PPI network in cystoscape and have used NetworkAnalyzer for network parameters such as Node Degree Distribution, Shortest Path Distribution, Betweenness Centrality, etc.
When ...
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1answer
57 views
Odds Ratio and gene mutations association
I have a simple (yet to me still trivial) problem to submit to you.
I have a dataset of a group of patients affected by a disease, for which the presence of several genes mutations was inferred.
Each ...
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2answers
65 views
What does the size of the Wilcoxon rank sum test 'W statistic' indicate?
I wish to see whether the average meal masses of two species are significantly different, and I have sample sizes of >800 for both. My Wilcoxon rank sum test returns a W = 330520 value - how should I ...
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1answer
9 views
Independence of time intervals in ANOVA?
I am not sure how the independence assumption in ANOVA applies in this scenario...
We have observational data on the foraging depth of whales across the summer separated into time intervals. We want ...
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0answers
22 views
How to properly analyze groups of cumulative dose-response curves in a 2x2 design?
We have data from following experiment: Animals were divided into 4 groups by combination of 2 factors (2x2 design). We then extracted 2 blood vessel rings from each animal (animal = biological ...
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2answers
95 views
Drawing conclusions of several inferences with the same data in one study
In a sample size of 100, we identified the existence of two attributes A and B.
Our goal is to assess whether there is any ...
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0answers
25 views
How to analyze size frequency data from over 70 sites
When I started my PhD, I had virtually no prep-time. My advisor needed me in the field and told me to go grab samples. As such, my planning wasn't the best, so sorry if this is a completely terrible ...
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20 views
How can I predict the gross profit of drug sales in these types of big Pharma datasets?
Suppose my dataset is of the following design:
Columns: Assumptions (Type of customers), Disease (What disease can the drug treat - one type), Location (a country), Value (the profit earned from the ...
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50 views
“Matching” with cross-sectional studies: are the samples dependent?
I am comparing the prevalence of disease in participants of two separate cross-sectional surveys. One survey is from a group of prisoners and the other is from the general population.
To account for ...
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9 views
How to find levels of a continuous biomarker for a categorical response
I'm trying to figure out what type of analysis would get me levels of a continuous predictor to parse my data into categories.
I have a dataset with progesterone (continuous predictor) and ...
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1answer
49 views
Expectation and variance of range (x(n)-x(1)) uniform [closed]
I am working on calculating the expectation and then variance of the range from a Uniform(-theta, theta) distribution, but have gotten stuck.
Basically the first page I show how I get the pdf and ...
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1answer
37 views
How to calculate confidence interval for proportions with small numerators and large denominators?
I'm working with summarized public health data, specifically mortality rates.
I have the numerators and denominators for each mortality, but that's it.
I'm stuck on what is the best method to ...
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1answer
201 views
Yeo-Johnson and Logarithmic transformation
Is a Yeo-Johnson transformation using a lambda equal to 0 the same transformation as a logarithmic transformation?
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47 views
Controlling FDR when p-values are bimodal
I have a quick question about using the Benjamini-Hochberg procedure to control FDR using the p.adjust() function in R. I have read that in order to properly apply ...
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21 views
P-value corrections when distribution is bimodal
I am analyzing a set of transcriptome data to assess which "GO categories" are significantly enriched using a tool called GOSeq (https://bioconductor.org/packages/release/bioc/html/goseq.html). Put ...
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2answers
65 views
McNemar's test probably does not work, but what could?
I have a dataset of people who had back-to-back procedures and I have the whether or not polyps (precancerous lesions) removed during each procedure.
...
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0answers
20 views
Demonstrate that a new non invasive test gives the same information of an invasive one
I'm planning a scientific study where I would investigate the correlation between a non-invasive imaging test with information taken from a CT scan.
My idea is to develop a study protocot, then to ...
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0answers
13 views
Pearson coefficient by averaging or concatenating time series
I record EEG signal from two participants. Each of them repeats the same task five times. Usually, I average all five time series for each of participant and calculate Pearson coefficient between them....
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1answer
122 views
GLM with a Poisson distribution, how to conduct a post-hoc test?
I have a dataset in which I compare the total number (the summed number of birds over a couple of weeks) of birds across different distances (continuous factor). I hypothesize that the numbers of ...
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22 views
Bayesian statistic in model comparison
I am trying to use the Bayesian statistic in model comparison.
Let's say I have 4 different pharmacokinetic models which I use to fit breast MRI data. Each of this model M gives me a certain number of ...
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0answers
24 views
Can proportional data be used in nonmetric multidimensional scaling (nMDS)?
I am using nonmetric multidimensional scaling (nMDS) to compare the diet composition of a predator at 7 different sites.
Each diet sample collected constitutes 1 meal. Each meal was made up of ~ 1-20 ...
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13 views
ANOVA or multiple regression? longitudinal study
I'm doing a longitudinal study of healthy patients (so I'm studying them over time ... say at age 7,8,9,10,11,12)
I think my independent variables would be: Age (continuous) and sex (2 categories)
...
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34 views
What is the most appropriate way to compare means when group size is markedly different?
This scenario seems to be arising more and more with the usage of large datasets in an attempt to identify pilot data for associations, etc. I'm trying to figure out what method - if any - is the most ...
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33 views
Which test should I use to compare 2 unrelated dichotomous variables?
I have two variables, both of which are categorical and binary/dichotomous, and I need to determine if there is any 'correlation' between them. Note that I am using this term carefully, as I know '...
