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

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Determine which diseases cluster together (binary data)

How do I determine which diseases cluster together? I have a dataset with patients and their diseases. It's coded as HOHT = 1 if they have it, and HOHT = 0 if they do not have it. Below is an example ...
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10 views

Cox regression groups

I have some experimental data for animals with tumours. Unfortunately, they were not followed individually during a time course, but evaluated as groups. As a result, I have 6 predictors only for ...
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16 views

Number of symptoms and genotype - what is the correct type of regression to use?

I apologise if I do not use the correct terms when describing my problem but hopefully you can help me. I have a data set with around 430 participants. They have given information on the number of ...
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10 views

Help with conditional expectation of a convolution of multiple exponential random variables with different parameters

I'm working through this paper, with lots of help from all the great people on this site. Obviously my statistics/probability is a lacking to follow all the mathematical steps. Currently, I'm trying ...
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1answer
29 views

How can standard logistic regression model fractional response variable while denominator is available?

I have X and Y variables, as well as a cluster variable (State). X and State are derived from Database A, while Y and State are derived from Database B. X is a sentiment score ranging between -1 and ...
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1answer
10 views

Which right test to choose

I am new in statistic and analysis, I have a question I wish to compare is the data from my Centre significantly difference with the data from the published paper. the number stated is the ...
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17 views

Are multiple testing corrections necessary when validating against an already processed and published database?

Short version: Do I have to apply multiple testing corrections when analyzing a single variable (from a multidimensional dataset) I have previously found to be relevant and validated in the lab using ...
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24 views

Taxonomy of statistical methods [closed]

Can someone point out to the scientific work that is methodologically developing and explaining the taxonomy of statistical methods? A similar question was asked here [1], however I am curious to know ...
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2answers
32 views

Creating clusters for binary data

I have a set of data with patients and their diseases. I would like to use hierarchical clustering or some kind of cluster analysis to make a dendrogram to see which diseases cluster together in this ...
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11 views

Which ANOVA model should I use?

I have a data set containing root, shoot, and seedling growth measurements from 5 treatment groups (at different concentrations, 3 replicates) including control. There were no separate control groups ...
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14 views

Should I use t-test or ANOVA+post hoc (two different treatments and a control)

I have been working with ice algaes,and Im looking on their fattyacids. Here is a bit about the experimental design. I have one treatment area, cleared, where I have removed all snow. I have ...
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2answers
49 views

Why do we need to model RNA-seq data using Poisson, negative binomial,

I am a biologist and use different packages like DESeq, ... to normalize my data and find deferential expressed genes. Recently I have started to learn probability and statistics and I have studied ...
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1answer
18 views

multiple testing with BH correction

I want to do genome wide association study. I have about 1,500,000 SNPs, and 36 samples with 18 from tumor cells and 18 from normal lood cells. We make fisher test or chi square test(we admit fisher ...
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16 views

In Complex sample analysis what is weight variable?

Using PPS sampling 30 clusters were selected from large province. From each cluster 40 individuals were randomly included in sample. Few clusters have less than 40 individuals due to some limitations ...
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2answers
109 views

Am I introducing bias by assuming birthdate is middle of month?

I have a dataset containing dichotomous disease measures as well as some continuous anthropometric measures on a cohort of patients, and includes their month and year of birth as well as the exact ...
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1answer
15 views

RNA-seq: Controlling FDR in multiple contrasts

I'm working on a RNA-seq analysis project and I have come across a statistics problem. I have 3 groups and I need to look for differential expression for each pairwise comparison. Do I control the ...
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8 views

RNA-seq: Controlling FDR in multiple contrasts

I'm working on a RNA-seq analysis project and I have come across a statistics problem. I have 3 groups and I need to look for differential expression for each pairwise comparison. Do I control the ...
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0answers
23 views

Variable selection methods for categorical predictors

I have categorical predictors only and the dependent variable is continuous. Which variable selection methods should be used for such model?
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1answer
34 views

When is it considered a repeated and independent experiment in chemistry?

Sorry for the somewhat confusing title. I was wondering about the use of confidence intervals in the context of chemical and biochemical experiments. The experiments must be repeated and the data have ...
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14 views

Analysing a three way interaction

Im currently analyzing a three way interaction in R and my data looks like this: ...
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0answers
15 views

GEEGLM, Gee - prezenting results?

Does anyone have experience with using generalized estimating equations and the gee and geeglm functions in R? If so, could you ...
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2answers
41 views

How to interpret geeglm results?

I have a question about the geeglm function in the GEE package in R. I am a beginner in statistics and the estimates in the output of the model are puzzling me. How ...
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49 views

Logistic Regression: What do people exactly mean by “cell size”? (example: small cell N's but no warning messages and convergence criteria met.)

I've been performing some logistic regressions and found some great results. The problem is I'm unsure if my model is stable or not. This is mostly because I am confused about what people mean by ...
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22 views

Dealing with seeming outliers in microarray gene expression data

I have the following microarray gene expression data for one gene let us say. BTW - have similar data for the same subjects across 17000 genes, so I am looking for a generalized solution. ...
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0answers
16 views

How to determine counts of viruses from limiting dilution assay

My question relates to a common experiment in the field of virology. Let me give some background so you understand why I'm asking this question. When producing virus for an experiment you typically ...
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13 views

Which statistical test for data comparison?

I have several sets (e.g. 100) of essential genes + non-essential ones, all were extracted from a certain database of essential genes for a particular disease under different conditions. How can I ...
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2answers
66 views

Confidence & conclusion in rare event analysis

I am looking at the http://www.nejm.org/doi/full/10.1056/NEJMoa021134 paper and don't understand how they made their conclusions. According to the data in Table 1 they analyzed 440655 vaccinated ...
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1answer
29 views

How do you appropriately adjust some variables in a regression that are normalized to a particular covariate?

If a variable is normally expressed relative to body weight and then I want to include that variable in a regression model that also includes body weight among other variables as covariates, do I have ...
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15 views

Unsure about what statistical test to carry out

I have a blood count data with a sample size of over 3000. I am dealing with these variables only: age, sex and WBC:Platelet(ratio). I am using SPSS and already done some descriptive statistical ...
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23 views

Log binomial regression with a case-control sample

It is my understanding that log binomial regression involves a direct comparison of prevalence ratios ("% cases among the exposed" vs. "% cases among the unexposed"), rather than using prevalence odds ...
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19 views

Normal vs. non normal distributed data. Choice of model

I have a question about normally distributed and non normally distributed data. I am going to do a genotype association analysis but I want to build a model for each trait that I have to know which ...
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48 views

Statistical modeling of biomedical data in industry and hospitals: scopes and ways to do so

I hope my questions still follows the guidelines of this community. It's about my job-search. I'd like to know whether and how statistical modeling of biomedical data are in industrial or hospital ...
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18 views

ANOVA on Delta Percentages

I would like to validate the effect of some drugs on a certain parameter in my cells. With the first drug, the parameter will go up, while with the second il will go down. The measurements have been ...
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0answers
14 views

Applying paired t-test to compare averages

So I did an experiment for 1 month where I investigated the change of pH of 3 different types of milk in the refrigerator and room temperature. I d now like to compare the results of each type of milk ...
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7 views

A rate model for sodium channels

I am studying by myself Human Physiology. I have encountered the following question: In the following given model of sodium channel with 3 states open closed blocked (which I assume means inactivated)...
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1answer
52 views

computing sensitivity, specificity, Positive predictive value and Negative predictive values of the test for presence and absence of the disease

A cancer screening test is being applied in a population of 200 men who were also evaluated through the biopsy of tumor. 30 of the men were confirmed having cancer through biopsy. Out of these 30, 25 ...
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1answer
20 views

What is the meaning of gradient & progression rate?

Event Rates Over Time for a 60-Year-Old Patient With Baseline Peak Aortic Valve (AV) Gradient of 25 mm Hg and Progression Rate of Aortic Stenosis of 5 mm Hg/Yr I have following questions: Q1. Does ...
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11 views

Is it valid to combine multiple columns for t testing when n is small?

I have measured one variable from 6 different samples each in three different patients. The 6 samples come three apiece from two different anatomic sites (blood and gut). I would have liked to use ...
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18 views

Mutations in known DNA sequence: which test to use?

I am analysing a double knockout (mouse), and trying to see whether restoring one or another of the genes it's missing affects specific positions preferentially in a third gene. The data* looks ...
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1answer
21 views

Given a biological dataset with measurements over a year, how can I identify seasonal variation, if any?

I have a biological dataset and I am interested in answering the following question: Are the measurements dependent on time-of-year/season? I use R for my analyses
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36 views

Tukey's test of additivity or Tukey's one degree of freedom test

Does anyone know anything about this test? I have a scale of 9 questions and I don't know how to explain Tukey's test of additivity or Tukey's one degree of freedom test. How to report this test and ...
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7 views

KAP survey: Best possible choice of analysis

What is the best way of doing data analysis for a KAP survey? Need to analyze the Teffect of intervention (health education) between the pre and post survey. Knowledge attitude and practice of 3 ...
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28 views

How to find the posterior distribution and posterior mode of Beta given an exponential prior distribution and binomial data?

This is the question I'm working on: I have already completed part (a). For part (b) i, I modeled y1 given Beta and n1 as Binomial(n1, p1 = d1/(d1+Beta)). For part (b) ii, I showed that the ...
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Variability of the reference data and its effect on the transformed values

I conducted a study to compare two different tests at two different ages (children). Based on the previous literature we had hoped that the scores should be better (low score) with age but this was ...
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35 views

Difference between Discrimination, Calibration, Accuracy and Precision

I have trouble understanding these terms: a.) Discrimination. b.) Calibration. c.) Accuracy. d.) Precision. I really get confused with the books I am reading, ...
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3answers
866 views

Statistical methods for data where only a minimum/maximum value is known

Is there a branch of statistics that deals with data for which exact values are not known, but for each individual, we know either a maximum or minimum bound to the value? I suspect that my problem ...
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18 views

Precision adjustment in biomarker analyses

In a causal modeling framework, we are concerned with measuring an association between an exposure and an outcome. To do that, we usually fit a regression model for the outcome as the "y" on the ...
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1answer
58 views

Fisher's exact test in RNA-Seq

In RNA-Seq analysis it is common to use tests analogous to Fisher's exact test to evaluate whether a gene is differentially expressed in two measured conditions. Fisher's exact test relies on ...
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0answers
19 views

Combining FDR value acquired from different microarray probes

Dear all great helpers, First of all, I would like to note that I'm quite new in Microarray analysis, and I hope you all be patient with me. I would like to provide an example and ask you all a ...
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35 views

Probability applied to cellular research

My friend reached out to me with this question, which he says is a simplified version of a cellular array question he is stuck on for his chemical bio research (Masters program). I have a grid of 10 ...