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

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Can I conduct multilevel analysis with two aggregated data sources?

I have two data sources with completely different specific individuals. One contains individuals answering whether or not they have watched the movie "Lego", and the other date source contains ...
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1answer
20 views

How to calculate mutual information from frequencies

Can someone explain to me how to calculate mutual information from contingency table? I have a contingency table containing counts from a sample of data And I want to calculate the mutual ...
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1answer
32 views

Find a window of ‘best correlation’ – exploratory analysis

I have data from a neurobiological experiment and I'm interested in learning which parts of multiple time-series (e.g. event-related potentials) best explain behavioural data (e.g. accuracy). Rather ...
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2answers
64 views

Can I apply statistics to catch rare diseases or make decisions about fate?

Suppose I am 50 years old and a study found that in my city 10 people (CI=4 people) die at 50. Now it's July and I have a very malignant disseminated cancer and this year 14 people died at age 50 in ...
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9 views

Hypothesis test design taking into account follow-up segmentation studies

Suppose I want to have a simple test with one treatment group and one control group. Let's assume the treatment for the treatment group is increasing a quantity $X$ by $10\%$. I have two questions: ...
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16 views

Are there any statistical fallacies that go with E-values?

I am presently learning how to use bioinformatics tools and among the first things to encounter was the notion of an E-value, explained on NCBI's help page for sequence alignment tool BLAST. As far as ...
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1answer
39 views

Bayesian biostatistics book

I am looking for a good book on biostatistics from a Bayesian point of view. I am going to be starting some research in oncology and so books geared towards that would be great, but also just a ...
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2answers
35 views

Which statistical test is appropriate for my data?

First 5 rows of my data are as follows: ...
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1answer
25 views

Is it possible to apply PCA to the reconstructed data of ICA?

I have read that it is not possible to verify the variance and order of independent component extracted from ICA. So, I reconstructed the spectra from matrix A and ST(independent component) then ...
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1answer
32 views

Can ANCOVA be used with a dichotomous dependent variable? If not, what have these authors done?

As stated above, if and how can ANCOVA be used with a dichotomous variable as the dependent/outcome variable? I found an article of which I wish to replicate some analyses ...
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16 views

How to calculate a score system

How can i create a scoring system using different variables (like score used in medicine)? I can calculate a regression equation but i'm having trouble converting this equation to a score assigning ...
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12 views

Prediction of one outcome using another

I have a general question. Suppose I have fit two separate longitudinal mixed effects models (say, model A and model B), they can both be simple and contain only time as a covariate. Say I have ...
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30 views

What is the impact of model accuracy on the reliability of random forest variable importance?

Just for some context, I'm asking this question from a biostastics perspective. Say you have gene expression data from multiple samples that fall under class A or class B. You then choose to build a ...
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17 views

Biasing regression by repeating variables

I'm building linear discrimination analyses and logistic regressions and I am trying to bias the regressions to favor specific variables. Each variable represents chemical information from a specific ...
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19 views

What kind of methods do I need to use in order to analyze this kind of health dataset

I've recently been given a dataset with the following variables: -BMI -Type of Therapy (indicated by 1, 2, or 3) -ADH Levels -HIV positive or negative (0,1 dummy variables) -Systolic blood pressure ...
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20 views

Statistical Analysis with repeated measures categorical data

For my Master thesis I looked at behavioral responses of fish by quantifying their position as a reaction to a certain treatment. I have 20 Fish that I measured on 7 consecutive days. Every day, each ...
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6 views

Power Calculation for Gene Significance

So, I think I need to do a power calculation for the following, but I am really not sure if that's the right procedure to use: I am looking at gene types in cancer, and I want to figure out if ...
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1answer
82 views

How to become a biostatistician? [closed]

What should a graduate student (MS in biostat) to be prepared to become a biostatistician? I've learn some statistics. But what I do now is just like statistician. I am just wondering what I should ...
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20 views

Trying to analyze a blocked, multilevel design with unbalanced, repeated measures

The research question(s): Do road crossings over streams influence the abundance of stream-dwelling salamanders (SDS)? Do these road crossings influence SDS abundances differently downstream than ...
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11 views

Pair-wise analysis with large amounts of data

I was asked to do a pair-wise analysis with target genes(~60) vs. a large amount of expressed genes (~4200). Can anyone shed some light onto what the most efficent way to do this is? I was going to ...
2
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1answer
32 views

What does 'Quantile Distribution' exactly refer to?

I am reading an article about normalization of next-generation sequencing (NGS) data (e.g. RNA-seq) where they use the notion of 'quantile distribution' (page 2). However, being a novice in the realm ...
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13 views

Is t-student enough for comparing these?

I'd like to compare two methods of measuring compounds quantity on chromatography paper, which we may call method A and method B (kind of like counting the same things using two different machines). ...
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1answer
24 views

In medical statistics, what is usually meant by “internal precision”?

I have come across the term "internal precision" in some books and papers and was wondering what this usually would refer to. Is there a standard definition for this term? Thanks!
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1answer
29 views

Comparing across groups and classifying (as in DFA) with non-normal data

I study birdsong, and am examining the structural song differences across multiple geographic groups (101 individuals across 3 groups), as measured via ~20 structure-related variables. I had hoped to ...
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58 views

Why using volcano plots in biostatistics?

In biology, it seems common to use a "volcano plot". Typically, it displays $-log_{10}(\text{p-value})$ in function of the fold-change (=difference of means between two biological conditions). See for ...
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76 views

Simple correlation coefficient between two time to event (survival) variables

I'm struggling searching for a simple correlation coefficient between two time to event variable, if available. All started with the need (from a clinical study) to check if the study end point is ...
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49 views

Adaptation of binomial testing: How-to?

My question arise from the field of genomics: Given that every chromosome exists in two copies, a specific feature can be present in 0 chromosomes (p=0) 1 chromosome (p=0.5) both chromosomes (p=1) ...
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19 views

Setting the conventional null hypothesis as the alternative? [duplicate]

I am a bit confused on assigning null and alternative hypotheses. For example in comparing 2 interventions, conventionally, null hypotheses are usually stating that there are no differences in ...
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2answers
39 views

Field or method to understand what independent variable affect the response variable the most

Say I have several bio-reactors (systems) and a bunch of independent variables which can be for example flux-intensity, rotational velocity in the bioreactor, nutrition etc. I also have my response ...
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2answers
40 views

Does this feel like Poisson regression..?

Suppose a particular gym has asked you to tell them about their gym members, specifically the gym members' use of the gym. And suppose they supply you with data describing a sample of gym members' ...
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0answers
11 views

Assigning score/values to a group based on its elements

I have three groups (group-A,group-B and group-C), each group contains elements with score/value for each element. For instance ...
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16 views

stats help please, looking to show similarity is not random

I have a gene of around 5000nt long and that gene can be compartmentalised in to around 20 various categories, however smaller strands of the gene called ‘motifs’ can be assigned to their respective ...
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2answers
172 views

Assessing the relationship between continuous variables

Age.of.Diagnosis Native.American European African 60 0.5 0.4 0.1 I have the ancestry data on ~100 individuals with ...
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1answer
39 views

Advanced/Professional online data analysis courses [closed]

I've been looking for some statistics, data analysis or other connected with bioinformatics field online courses. Unfortunately, many of them have an introduction or beginner level (like on coursera) ...
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38 views

Test for very small sample sizes

I did home range estimations with 4 individuals and I struggle to find a proper test to test if they differ significantly. My data looks like that: ...
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13 views

Sparse Contingency Table Analysis

I am relatively new to categorical data analysis and was looking for some opinions on my analysis approach. I have 4 categorical variables, OUTCOME, X, Y, and Z. All are binary except for Z which has ...
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32 views

3-way ANOVA to 2-way ANOVA

I have an experimental design with 3 factors of 2 levels each, which are temperature (a1 & a2), pH(b1 & b2) and food (c1 & c2), so I first ran a 3-way anova. Since in 2x2x2 experimental ...
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2answers
69 views

P-value versus Exp(B) value in Cox regression analysis

I performed Cox regression analysis for two Biomarkers. Both were significant (p<0.05). Biomarker 1 showed higher significance but lower Exp(B)=hazard ratio value than Biomarker 2 (see below). ...
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118 views

What's the most adequate test/tests for this study?

I'm a PhD student (Biodiversity and Animal Ecology). I am preparing a scientific article to submit and I need help in statistical analysis of my data. In this message I will try to provide as much as ...
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2answers
68 views

How to compare these bioinformatical categorical data

I have the information for 100 positions in the genome of 10 cases and 10 controls. The response for every individual and each SNP (Single-nucleotide polymorphism) position is 0, 1 or 2 (these ...
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0answers
52 views

Association analysis of different angiogenic markers with different time points

I would like to know the statistical tests which can be used to measure the association of the angiogenic measurements, measured at five different time points, with a biomarker. ...
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1answer
17 views

How to connect groups if they are not large enough?

I am new at statistics and I have problem that I have no idea how to solve. I have biological data, which includes expression levels (130 patients) for different alleles (I'm analysing SNP's) of ...
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27 views

Binary logistic regression - SPSS

I did some regression analysis in SPSS using two binary variables: Biomarker X (0= low levels; 1= high levels), where 0 was the reference category and Obesity (0=no; 1=yes) ''Biomarker X'' was taken ...
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1answer
47 views

Whether or not to use a multilevel (hierarchical) model

I have a dataset, and I am not sure whether I have to use a multilevel(hierarchical) model or not. Suppose I have 10 dishes with a cell culture in each dish, and of these 10 cell cultures, 5 are ...
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2answers
54 views

How to define clustering in R

The data contains information about the genes causing breast cancer in our body. My aim is to find the most effective gene on breast cancer in our body. The code that I have first divides my sample by ...
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23 views

The best model to analyse this data set: Comparing bacteria communities within calves

The design is like this: I have 18 calves in the experiment, and all these calves were divided into 3 groups with 6 calves in each group. The 6 calves in group 1 were euthanized at the end of the ...
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0answers
72 views

Interpreting a qq plot

Simple question, I'm new to biostatistics and the interpretation of qq-plots. What does this qq-plot say about the distribution of my sample? Is it bimodal?
4
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1answer
68 views

What is the reason for the shape of the volcano plot?

I use it in biostatistics. For example, why do genes (or any input value) with a larger absolute fold-change also tend to have a more significant p-Value? All volcano plots look like it, so I assume, ...
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0answers
34 views

Which statistical test to use for comparing frequency of cells in four different sample groups?

I am currently writing up my thesis for my MSc and I wondered if someone could help with the type of statistical test I should be using and why. I am not very good at the statistics part and any help ...
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27 views

Normalization/Multiple Regression Question

I work in cell culture and normally don't have to use anything more than T-tests, but this project has me stumped... The study design: 1 control treatment and 7 experimental treatments with one ...