Questions tagged [statistics]

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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 (...
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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-...
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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
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 ...
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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 ...
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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 ...
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2answers
176 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
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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 ...
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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 ...
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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 ...
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How are the values of prop.part() and prop.clades() calculated?

Consider the following dataset: ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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1answer
65 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
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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 ...
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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/...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 (...
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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 ...
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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
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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
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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 ...
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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 ...
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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 ...
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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 ...