Questions tagged [biostatistics]

The branch of statistics that deals with data relating to living organisms.

16 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
26
votes
1answer
2k views

Additive genetic variance components from LMER in R

I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be ...
3
votes
0answers
283 views

Is there a standard formula/calculation for sexual dimorphism?

Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use $$\frac{\text{Female value}}{\text{Male value}} -1$$ This would give negative values ...
3
votes
1answer
193 views

How to interpret Glimmer scores?

I am trying to find orfs with Glimmer. At the end, Glimmer gives me a .predict file with the orfs and a corresponding raw score. When I look at the documentation, it says about the score, "This is ...
2
votes
0answers
29 views

To what extent does the distribution of nerual transmiters in the brain vary human to human?

Suppose $x$ is a position in the brain, and $n_i(x)$ is the density of neuro recepter $i$ around that point. Any given human will have some distribution of neruo recepters $n_i(x)$ through out there ...
1
vote
0answers
20 views

How many samples to run an association study on B-Cell receptors

We are trying to find biomarkers on the B-Cell receptor VDJ regions. To do this we plan to run Single cell RNA-Seq (using the solution from 10x genomics https://www.10xgenomics.com/solutions/vdj/) to ...
1
vote
0answers
211 views

How to correlate survival probability to gene expression profile?

I am reading up survival analysis of cancer patients and correlating them to gene expression. I came across this tutorial. Its mostly code. So what I still have not been able to understand is how ...
1
vote
0answers
30 views

Fisher's Method to melt p-values for CpG sites annotated to the same gene?

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
1
vote
0answers
47 views

Replication cohorts in microbial GWAS

Replication in an independent cohort is of course the gold standard in GWAS studies, and many high profile journals will now (quite rightly) not accept finding indicating a phenotype genotype ...
1
vote
0answers
256 views

Using Chi-squared analysis to confirm expected phenotypic ratios of offspring

In a recent question the original poster was faced with deciding which ratios to use in a Chi-squared analysis. They were supposed to decide on, "logically", what test-ratio to use. Example question: ...
1
vote
0answers
125 views

Biological replicates

We are currently doing an screening where supernatans from a bacteria genus are tested againts a pathogenic bacteria cell culture in a 96-well plate where OD is measured each 2 hours. Each ...
1
vote
0answers
80 views

Large set of semen microscope images needed

As a course project I have to write an algorithm whose purpose is to analyze a sperm sample (total number, motility etc). In order to do that though, I need to have a sufficient number of images to ...
0
votes
0answers
27 views

Is it scientifically feasible to compare two samples of different sizes, while values in each sample are average numbers?

I want to compare result from my protein docking experiments to various protein structures of the same protein. I have two samples and in Sample 1, I have ...
0
votes
0answers
25 views

Help on selecting 2 tests - unsure if they are paired or non-paired statistical test

I have data that measures the temperature of flowers and leaves on different plant species. These are the comparisons I am trying to make: Comparing the flower and leaf of the same plant at the same ...
0
votes
0answers
17 views

Can anything useful be done with stable isotope data for a single species

This is my first biology question. So I have some stable isotope data on a single species. This data looks similar to the demo data in the siar package for r which looks like this: ...
0
votes
0answers
32 views

Frequency of nucleotide sequences of specific length in DNA

How frequently would you find the nucleotide sequence GGATATCCGC (5' to 3' direction) by chance in a DNA molecule? On average, how many times do you expect to find a specific 20 nucleotide sequence in ...
0
votes
0answers
44 views

Is it okay to scale the RNA-Seq counts after log-transformation?

On an RNA-Seq dataset, I want to apply a clustering algorithm which requires zero-mean uni-variance gene expression levels. I am wondering whether it makes sense to use "scale" function in R after ...