Questions tagged [statistics]
For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
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Identifying substrates with enriched degradation potential from count data of enzymes able to degrade that substrate across all samples
How would I identify if I have enriched degradation of a certain substrate within a clade of bacteria with count data of enzyme capable of degrading a range of substrates?
I have started of by ...
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22 views
Non-finite value supplied by optim in Hurdle model of enzyme count data
I have a dataset of enzymes counts that are grouped by substrate they degrade and am attempting to model if the origin of the genome in which the enzymes were found can predict the count for ...
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2answers
37 views
What does aov(glm model) actually do in R?
What is happening when you use aov() on a glm model in R?
Normal glm model sumamry(m1):
...
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2answers
30 views
Determining significance of a variable in a glm model
How would one determine the significance of a variable in a glm model?
If I, for example, have a dataframe like seen below, how would I determine if the origin of the sample has a significant effect ...
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1answer
37 views
How do I set a neural network to loop multiple times and average the resulting values?
I have a script in R/RStudio which creates random datasets of binomial variables, feeds them through a neural network, and calculates their likelihood ratio statistic and deviance. I'd like the script ...
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1answer
16 views
Is outlier detection the right choice for determining if a value lies singificantly away from the mean in a population in gene frequency?
I have the following dataframe that is comprised of enzyme substrates as the variable and then the unique number of times enzymes capiable of degrading this substrates appeared in my genomes and then ...
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27 views
Regarding RNA seq data analysis and building coexpression network
I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot.
I am currently normalizing RNA seq data for comparing genes expression within and between samples. ...
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1answer
34 views
3
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1answer
48 views
Inflated p-values in quantitative trait analysis
I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders ...
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2answers
52 views
Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)
Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the ...
2
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1answer
39 views
When should I apply a multiple comparison adjustment?
I am performing a RQL analysis ("http://www.esapubs.org/archive/ecol/E095/002/suppl-1.pdf").
This analysis meassures the relationship between different traits of three different matrix showing if ...
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2answers
22 views
Should you filter GWAS hits with high standard error?
I'm trying to figure out if I should be filtering out GWAS hits that have high standard error and I'm not quite sure what to do. It seems like it might not matter, because the standard error is used ...
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1answer
18 views
Arlequin files not able to converge beyond 2000 steps for some .arp files
When I use .arp files in arlequin to run mismatch distribution it says that can’t converge beyond 2000 steps and also no graphs are produced.can someone suggests what can I do to overcome this problem
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1answer
30 views
How to run Cox proportional Hazard model for each group in R?
My population is divided into 10 groups. I want to run the cox-proportional hazard model separately for each of these 10 groups so that in the end i can compare which groups has highest hazard ratio ...
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2answers
79 views
What is the difference between fixed effects and random effects in the context of Linear-mixed models?
The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
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1answer
35 views
How to compute Shanon entropy
I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
3
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1answer
99 views
Comparing phylogenetic models with different datasets
I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
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1answer
131 views
Prediction model for spread of coronavirus
A previous thread on Bioinformatics StackExchange citing an article by the Economist which references a cartoon of predictive outcomes by the CDC (Economist article on coronavirus) suggests a model in ...
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1answer
75 views
a package with randomization/permutation tests for genomic analyses
please would you let me know, is there a package in R/python/C that has implemented randomization/permutation tests for joint genomic analyses
(an example of joint genomic analyses -- when jointly ...
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2answers
182 views
Economist article on coronavirus
I am wondering about an article in the Economist here:
https://www.economist.com/briefing/2020/02/29/covid-19-is-now-in-50-countries-and-things-will-get-worse
There is a graph there
The explanation ...
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1answer
64 views
How to deal with zeros in the denominator when calculating percent enrichment?
I have a data.frame with results from a CRISPR screen.
I want to calculate the % enrichment of a variable of interest var from ...
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3answers
569 views
Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?
When calculating how lethal a virus outbreak is, I've noticed that most sources use
CONFIRMED_DEATHS/CONFIRMED_INFECTIONS
However, given that there are only 2 ...
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2answers
44 views
How to exclude the repetition of gene-gene correlation calculation in python?
I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my genes, ...
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3answers
206 views
Is it possible to do this in R?
I have a big clinical data file with 96 columns like age, gender, BMI, etc
I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
2
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2answers
43 views
Most scalable pseudotime ordering algorithm
What algorithms for linear Pseudotime trajectory construction (diffusion-based) are the most scalable to large datasets?
I'm currently using Slingshot based on the recommendation in this manuscript: ...
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0answers
11 views
Quartert and Statistical Consistency
I found that triplet is statistically consistent, meaning, Given large amount data, most occurring Gene tree containing three taxa will likely be a true species tree I understand the proof. Is ...
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1answer
40 views
Use of Electronic Phenotype in EHR
May I know what's the use of Electronic Phenotyping using EHR data?
I did refer this link but have few questions
I understand that ...
3
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1answer
72 views
protein secondary structure matching/comparison scoring
I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.
Example:
...
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0answers
10 views
Recalculating fold change in microarray from a subset of samples
I have some bulk microarray data that I have pulled from online sources which describes the spatial distribution of transcription. The tissue in question has a few different subregions. I am ...
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0answers
43 views
Detect differentially expressing cells
after comments on my original post, I will ask my question again here
I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
2
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0answers
38 views
Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python
I am attempting to write a tool to be used by my lab to automatically generate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
3
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1answer
62 views
What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?
This question was also asked on Biostars
I'm trying to understand what is the best algorithm for GWAS nowadays.
I know we have many tools available like Plink and Hail, but currently, what is the ...
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1answer
50 views
Interpreting a kernel density function plot of gene expression
I need help interpreting a kernal density plot and a histogram of this data. I have provided some context below let me know if you need more information
A co-worker that I am collaborating with has a ...
1
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2answers
57 views
Normal score transformation
This question is related to a normal score transformation which is performed in the paper by
RUAN, Quansong, et al. Local similarity analysis reveals unique associations among marine bacterioplankton ...
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0answers
80 views
Should I use log2-CPM values (voom-limma) as input for my model?
We have created a model to integrate several OMICs data, but we realized that the maximum TPM values of RNA-Seq data were so big that had unexpected effects on our results. We hypothesized that this ...
2
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1answer
66 views
How to interpret Mendelian randomization results?
I did Mendelian randomization using this software:
https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf
...
3
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0answers
23 views
Find covariation of different DNA-binding protein binding between two conditions
I have ChIP-seq data of RNAPII and two other factors which we think follow RNAPII during transcription in two different conditions, and I'd like to show that the genes that lose RNAPII also lose the ...
2
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1answer
181 views
Confidence Interval with Wilcoxon Test in Python for log-normal Distribution
I have a couple arrays of dN/dS scores, and I would like to calculate the confidence interval for each array of data. dN/dS scores are not normally distributed but are log-normally distrbuted, so I ...
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1answer
116 views
Biplot scores from canonical correspondence analysis
I'm using the R package vegan to perform canonical correspondence analysis (CCA). As input we have two matrices, one being (sites)x(species) and the other being (sites)x(conditions).
Sample data (...
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63 views
length of 'dimnames' [1686] must match that of 'dims' [3]
Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion.
...
2
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1answer
410 views
Create a Grouped Barchart
I’m trying to create a Group Chart like this:
I have 7 classes for each of 4 species, not 5 like in the diagram. I want to build i diagram to show the distributions of the classes in each species
...
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1answer
35 views
Total read count of shotgun affected by few highly abundant sequences
I am building statistical models to analyse output from Illumina shotgun sequencing (HiSeq 4000) on stool samples (but RNA-seq data should behave similarily). The raw counts are a statistical sample ...
2
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1answer
115 views
How are residuals used as new phenotype?
I'm a novice trying to wrap my head around with fancy jargons. If I search residual, I understand that it represents the difference between the observed value of the dependent variable (y) and the ...
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17 views
Statistics in EGSEA
I am not sure if this question should be posted here or cross validated so please move if it is not appropriate.
I am planning to use ensemble of gene set enrichment analysis and trying to understand ...
2
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0answers
40 views
Number of reactions per metabolic pathway
What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database (kegg, metacyc,reactome..) is more helpful/reliable for ...
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2answers
65 views
Statistical test design question
I have condition as such mouse liver and spleen data.
So in liver I have WT (Wild Type) and KO (knock out) as well as in spleen WT (Wild Type) and KO (knock out).
I have to compare the parasite load ...
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61 views
Which statistical test to use for comparing two groups?
I have data for 396 transcriptional factors (TF), where I have calculated the number of Transcriptional targets for each transcriptional factor present between the two groups:
Group-I(G-I): where co-...
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49 views
What are the mathematical assumptions and algorithmic procedure behind MACS2?
I wonder if there's some mathematical details that outline what the algorithms does.
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2answers
108 views
residual Squared Coefficient of Variation (rCV²) vs Distance to Median (DM)
I am working with single cell RNA-seq data. I obtained the squared coefficient of variation (CV²) as a measure of gene expression variability:
I want a metric to express gene expression noise that ...
2
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1answer
99 views
Significant gene set testing - limma
While I have used my title, it is more of a general statistics question regarding how these significance tests are carried out, these include decideTests and ...
