Questions tagged [statistics]
For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
66
questions
2
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0answers
11 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 ...
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20 views
What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?
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 best algorithm if I won't use any them? Let's ...
0
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1answer
34 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
vote
1answer
27 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 ...
1
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0answers
20 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 ...
1
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0answers
31 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
votes
0answers
22 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
votes
1answer
32 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 ...
0
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1answer
35 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 (...
0
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0answers
49 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
votes
1answer
67 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
...
1
vote
1answer
29 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
votes
1answer
45 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 ...
0
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0answers
13 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
votes
0answers
38 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 ...
0
votes
2answers
56 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 ...
0
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0answers
54 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-...
1
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0answers
37 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.
0
votes
2answers
56 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
votes
1answer
85 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 ...
3
votes
1answer
218 views
Understanding PCHeatmap outputs
I am currently trying to understand the purpose of these PCHeatmaps - part of the seurat package in R:
All the online documentation I have searched for has only ...
0
votes
2answers
176 views
1
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1answer
112 views
Extracting genes differentially expressed by Wilcox test
I have 2 cell types (NOF and CAF) cultures individually and also have been co-cultured with tumour like this picture.
https://ibb.co/x8Ty1Wz
If this is the log cpm of these 4 samples
...
2
votes
2answers
113 views
Genomics Statistics Problem
I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding.
I have identified 728 sequences of interest. 597 of these ...
1
vote
1answer
40 views
Continuing analysis based on a log-likelihood ratio? (Comparing methylation between two PoolSeq phenotypes)
I'm trying to get some pointers on where to start on the analysis of my dataset. First, some basic info:
Background:
We performed Nanopore sequencing of two poolseq samples called UU and DD referring ...
3
votes
0answers
34 views
2
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1answer
788 views
3D PCA group labelling
I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA
...
4
votes
1answer
54 views
Why are my Chi-squared test results different from those in a published table?
I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation ...
1
vote
1answer
31 views
What does it mean for an amino acid to match with itself 99% of the time in a PAM1 matrix?
In this video, the lecturer says:
You see that phenylalanine is probably still phenylalanine because only one percent of amino acids have changed so roughly 99 percent of the time, phenylalanine is ...
2
votes
0answers
53 views
Block wise protein imputation
I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The data is perfectly balanced between blocks, with equal treatment representation in each block. Each block ...
2
votes
1answer
55 views
How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?
Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated?
What is meant by ...
3
votes
0answers
38 views
What is the correct way of dealing with the analysis of data from flow cytometry?
I would like to detect a change in expression of a molecule present on a cell type by flow cytometry.
Assuming I am able to detect, using an antibody, a signal that represents the amount of the ...
5
votes
1answer
175 views
Should PCA be standardized for gene expression?
This is a theory/good practice question more than a technical one. If samples are being plotted on a PCA projection of gene expression data, I'm wondering whether it is standard (and if so, why) to ...
1
vote
1answer
69 views
A basic question about phylogenetic inference with Bayes-MCMC
I am new to the world world of Bayesian-MCMC inference and have been working my way through various texts. I am having some difficulty understanding how MCMC works. I understand that it is a way of ...
1
vote
1answer
65 views
2
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0answers
40 views
Correcting for noise in RT-qPCR gene expression data
I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a logistic regression classifier.
I also ...
1
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0answers
21 views
Any input as to what to study in order to work into genetic engineering from math background?
Any input as to what to study in order to work into genetic engineering from math background?
I have troubles understanding what the "interface" would be between mathematicians and biologists/...
3
votes
1answer
145 views
Test to determine if two genes/exons share the same evolutionary histories?
In classic phylogenetic inference one is usually given various orthologue sequences of a given gene across various species.
Those sequences are then multiple aligned and used to construct a ...
2
votes
0answers
65 views
Is there a way to do GWAS on phenotype data that is not normally distributed?
Is there a way to do GWAS on phenotype data that is not normally distributed?
For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00. Or, perhaps ...
4
votes
1answer
90 views
LRT or LRT-like test on cyclical (Sleep) data
I have RNA-Seq data from 4 time points (3 hours awake, 9 hours awake, 3 hours asleep, 9 hours asleep). I'm interested in doing something similar to a LRT where genes are found to be significant if ...
6
votes
1answer
305 views
Intuitive explanation of GSVA analysis
I'm trying to understand the way the GSVA analysis is working behind the scenes.And I was wondering if there is any way to understand it more intuitively the whole process.
So at first according to ...
1
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0answers
80 views
Normalize before using adonis?
I'm using adonis, an implementation of MANOVA in R (vegan package) to understand how continuous (temperature, pH) and ...
1
vote
1answer
280 views
Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment
My task is to count the mutations occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (...
4
votes
0answers
45 views
Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?
I'm running the pathifier approach against C2 pathway curated
database for a specific microarray dataset.
As I was reading the documentation of the pathifier, in order to configure it properly for ...
8
votes
1answer
299 views
Comparison of gene set enrichment statistics
I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
8
votes
2answers
239 views
Comparing two genome annotations
I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
3
votes
1answer
111 views
Matlab scatter diagram
I have two columns of data, x and y, how can I make a ‘thermodynamic diagram’ with matlab? The z axis is the density value of dots, like below figure.
The x-axis is angle, y-axis is distance.
I want ...
1
vote
2answers
126 views
Can structural equation modeling be used in Bioinformatics?
I am a bioinformatics student and I was learning the basics of structural equation modeling (SEM) to help one of my friends.
I was wondering, are there any applications of SEM in bioinformatics? Any ...
2
votes
1answer
117 views
Why do I obtain very strange results with DESeq2?
I am using DESeq2 to perform a differential expression analysis, but I obtained very strange results for some genes. For some genes, I have very high log2FoldChange with very low p-value as displayed ...
4
votes
1answer
73 views
Standard Cutoff for Moderated T-statistics
I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma.
Is there any standard practice for where to cut off that value? For log2 fold change I ...
