The study of the collection, analysis, and interpretation of data.

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22
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3answers
2k views

Is it necessary to conduct a power analysis before beginning an experiment?

I know that power analysis is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power ...
11
votes
2answers
2k views

What is the difference between naive and adjusted p-values in a GWAS study?

What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from this paper: After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) ...
10
votes
3answers
694 views

How best to count bees entering and leaving a hive to measure hive activity?

This is my first question here, so I apologize for all mistakes I could have possibly made. I'm a high school student in East-Central Europe and I need to complete some research for a biology contest ...
9
votes
1answer
169 views

Systems identification in small neural network

When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current ...
9
votes
1answer
107 views

What is the base cancer rate for an arbitrary carcinogen?

Are all carcinogens equally potent? Is the relationship between dose and probability of cancer roughly equal, or are there some carcinogens that provoke cancer significantly more than their cousins?
9
votes
1answer
833 views

How does population stability evolve?

The number of individuals constituting a population is called population size. Over time population size does not remain constant, it fluctuates to different extent over generations because of ...
9
votes
2answers
80 views

Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?

I have been reading with fascination about the several molecular- and cellular-scale mechanisms and structural changes that underlie what we refer to as long-term plasticity. For instance, [1], [2], ...
8
votes
1answer
621 views

A timeline of the odds for survival for fertilized eggs and fetuses

I'm looking for data to build a timeline of the odds for survival of a fertilized egg, i.e., What are the odds it'll last a week? What are the odds it'll last a month? 2 months? (and so on ...
7
votes
2answers
121 views

A mathematician's confusion regarding parametric $t$ tests for gene expression data

I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as Sotiriou et. al. to understand what is typically done with such data sets. ...
7
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1answer
135 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
7
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0answers
42 views

Biostatistics: Pollen dispersal directionality

What Information am I looking for? Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around ...
6
votes
1answer
615 views

What is Mendelian Randomization, and how is it used to infer causality in epidemiology?

Studies of human traits and diseases are inherently confined to observational studies, known as epidemiological studies. This can make it very hard to determine what actually causes a particular ...
6
votes
2answers
234 views

Can I compare Shannon indices of metagenome gene data?

I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the ...
5
votes
1answer
39 views

Are there any online resources one can use to access raw clinical trial data without having to contact those involved in the study?

I want to do some statistical analysis and I have a preference for real data so I was wondering if there's somewhere I can get such data for free without a heap of bother in phoning other those ...
4
votes
1answer
1k views

What does conditional analysis of a SNP in a GWA study entail?

I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term "conditional analysis" used without any ...
4
votes
1answer
81 views

Why estimate linear and full (linear, quadratic, and correlational) selection coefficients separately?

"We then fitted a linear regression including all three life-history traits to estimate the vector of linear selection gradients, β, for each sex (Lande and Arnold 1983). A quadratic regression ...
4
votes
0answers
44 views

Statistical method for characterizing the relationship between body mass and metabolic rate

There is a dataset that contains body mass ($x$) and metabolic rate ($y$) from many different organisms. It is common to fit the data to the model of the form $y=ax^b$ and estimate the parameters $a$ ...
3
votes
2answers
80 views

Choosing appropriate statistical test for ordinal data

Ordinal response variables show up often in biology, but I'm not sure how they are best analysed. Some examples are qualitative assessments (little, many, a lot) or risk assessments (low risk, medium ...
3
votes
1answer
968 views

RNA-seq analysis - q-values in cuffdiff

I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change ...
3
votes
1answer
70 views

What equation to compare protein isoforms in a Western Blot?

The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks ...
3
votes
1answer
125 views

Are people genetically predisposed to being interested in specific fields/ideas? How does specialization occur?

I'm not sure if I formulated my question well, but I'm curious about a couple statements made by Steven Pinker and and James Heckman. In this interview: ...
3
votes
1answer
738 views

Index of ecological niche overlap

For this question I am interested in the Pianka's Index of ecological niche overlap. What is the Pianka's Index? How does it work? How can one calculate this index? How often is it used? In what ...
3
votes
1answer
87 views

What is a good source for info on disease frequency distribution among age groups?

I need information on the disease frequency distribution among age groups for an Android app I'm building... Hopefully I've come to the right place. Is there a good data source for this? Like a ...
3
votes
0answers
85 views

Data analysis of transcriptome sequencing data [closed]

I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are ...
3
votes
0answers
1k views

What are the factors to consider when determining the sample size for a given study?

Say I'm designing a retrospective study (where I'd collect data from various schools for the last 5 years) to see if consuming milk can contribute to childhood obesity. How do I decide on how many ...
2
votes
1answer
192 views

Two brown-haired people have two children, P and Q. P has blond hair. Q has brown hair. What is the probability that Q is heterozygous?

Two brown-haired people have two children, P and Q. P has blond hair. We therefore believe that each parent is heterozygous and that blond hair is a recessive trait. Q has brown hair. What is the ...
2
votes
3answers
316 views

Why cancer mutations do accumulate sequentially?

According to Knudson hypothesis, cancer mutations accumulate in order. Statistics says, that cancer probability increases as sixth order of age, which may mean six consequential steps to cancer. But, ...
2
votes
3answers
366 views

Where can I find a list of diseases and their incidence?

Say I am studying a particular disease and I know that its incidence is 0.8 per 100000 children below the age of 18, how would I find the incidence of a whole bunch of other pediatric diseases (or ...
2
votes
1answer
37 views

Correct/complete representation of RTPCR statistics

In papers reporting a relative quantification of gene expression by RTPCR, I often see a bar chart with mean ± standard error or deviation, with the deviation belonging to biological replicates. This ...
2
votes
1answer
41 views

Data Bias in protein-protein interactions data

Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?. a)The first is gene co-occurrence ...
2
votes
2answers
110 views

What are the statistical tools for distinguishing molecular analogy from homology?

Scientists have developed statistical tools that distinguish "distant" homologies from coincidental molecular homoplasy in extremely divergent sequences. What are these tools?How are they used ? I ...
2
votes
1answer
36 views

Material on the analysis of (micro)array data

I'm at the moment analyzing cytokine array data. The available material on the statistical analysis of these data is more than unsatisfactory. Since a lot of effort is being made in the analysis of ...
2
votes
1answer
37 views

Comparing gene expression levels between control and disease at different time points

I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group. I want to identify the changes ...
2
votes
1answer
101 views

(Updated question) Problem with Fold-change mean compared to absolute data (in qPCR)

For the problem below I am aware of the statistics involved but just can't get my finger around the following: In biology we use qPCR to measure gene expression or basically number of mRNA copies. It ...
2
votes
1answer
42 views

What are the benefits of statins in terms of prolonging life?

Recently the UK government suggested that all adults over the age of 50, without exception, would benefit from taking statins. I have an elderly female relative who may, or may not have had a minor ...
2
votes
2answers
48 views

Valid comparison of gene expression between several genes in several cell lines

We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes. Our goal would be to be able to compare relative gene expression for genes over the ...
2
votes
2answers
78 views

Tree census data for Sweden/Scandinavia?

Is anyone aware of any attempts to count or approximate the number of trees there are in Sweden or Scandinavia? I have a small popular science side project for which this would be useful
2
votes
1answer
81 views

What type of distribution should binding affinities fit?

I've been averaging Ki values from the PDSP Ki Database, and I can't help but to wonder: how I can determine p values for the binding affinities, so I can exclude anomalies in the data if need be?
2
votes
0answers
30 views

Using Canonical Correspondence Analysis on matrices with missing data

I have a matrix of sites where not all the environmental variables I want to assess were sampled. In other words, there are sites with the whole set of variables sampled, and there are other sites ...
1
vote
2answers
82 views

Cancer cure statistics questions

I have a question about cancer cure statistics. Many of the cancer literature or databases I have come across speak about 5 year or 10 year survival rates. In this case survival means that the patient ...
1
vote
1answer
71 views

Appropriate statistical test for a student lab?

I am a HS Bio teacher and doing a microevolution lab involving candy. Essentially students use four candy types and push them together until one cracks (Nat Sel). They also do simulations of ...
1
vote
1answer
446 views

How many (taxonomic) families are there?

Approximately, how many families have been identified? I've often often come across figures for the total number of species on Earth. Recently, I found myself wondering about the encompassing ranks ...
1
vote
1answer
49 views

About validation process of phenological study

I have recently done a phenological study using remote sensing techniques. Now I need to validate my results and my methods, that is, to determine if the phenology estimated from remote sensing is ...
1
vote
1answer
89 views

How do I compare the variance of a distribution of species in one area versus another?

It's possible that this question is better suited for stack overflow, but I think the ecologists on this site might be better equipped to answer it. I'm trying to study two geographically-isolated ...
1
vote
1answer
132 views

Standardized Selection Ratio (SSR)

In this article the athors used the Standardized Selection Ratio (SSR) in order to infer what is the preferred host (anemone) of anemonefish. Here is a quotation coming from their methods: ...
1
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0answers
19 views

How to study the number of herbivores per type of tree and time of day?

Suppose I want to find out the number of herbivores in different kinds of trees, and also compare the numbers between day and night. How would this kind of study be run in practice? It easy to think ...
1
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0answers
38 views

Cigarette consumption dose-response function WRT health outcomes

I'm curious how health risks (mortality, lifetime probability of cancer, etc) change with cigarette consumption. Specifically, treatring cigarette consumption like a continuous variable, rather than ...
1
vote
0answers
45 views

“Gold standard” for CNV detection methods?

Is there a generally accepted "gold standard" for testing the performance of CNV detection methods? I'm interested both in learning about existing datasets that may serve as gold standards for CNV ...
0
votes
1answer
86 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
0
votes
1answer
61 views

Needing help in order to infer the statistical hypothesis tests performed in an old paper

I am in great need of help in order to infer the statistical hypothesis tests performed in an old paper. However I need to make some reasonable guesses only from the abstract of the paper since the ...