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Questions tagged [biostatistics]

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

26
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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
1answer
182 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
1answer
575 views

What is the formula to establish ec50 reproducibility with respect to dose response curves for some drug?

The EC50 is determined by fitting a standard curve to the experimentally obtained control values for each dose response curve using some software that does trial and comparison until satisfactory(...
3
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0answers
274 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 ...
2
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0answers
26 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 ...
2
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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
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0answers
18 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
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0answers
195 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 ...
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0answers
46 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
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0answers
249 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
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0answers
109 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 ...
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0answers
76 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 ...
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0answers
62 views

Do (sexually) transmissible diseases spread more quickly through smaller, more connected communities, like the homosexual community?

This article implies that "when you’re meeting a guy for casual sex, the pool of people you have to choose from is smaller" and this is something which "allows HIV and other STIs to spread quickly ...
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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
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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 ...