Questions tagged [statistics]

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56 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". ...
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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
161 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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3answers
282 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 with a long ...
4
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1answer
114 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
663 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
140 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
439 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
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1answer
61 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 my ...
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1answer
451 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 ...
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2answers
312 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/...
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1answer
550 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
155 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). I was wondering, are there any applications of SEM on bioinformatics? Are there any strong sides ...
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1answer
265 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
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1answer
128 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 ...
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2answers
369 views

pvalue calculation of protein-protein network with permutation test

Note: this question has also been asked on Biostars I have performed a network recreation analysis based on the interactions of proteins from String db. I wanted to know if the interactions have ...
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1answer
58 views

What is the significance of the effect size on WOMAC scores for TKA?

https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210 I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on ...
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1answer
972 views

Adjusting phenotypes by regressing out covariates

I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and github). In the user manual, it states: We recommend first ...
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1answer
130 views

What will be an appropriate mathematical distribution for SNP data?

I found that several papers describe SNPs as a binomial distribution with the probability of "success" equals to minor allele frequency. However, in my experiments, when I generate SNP array ...
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2answers
2k views

What is the best distribution to model the FPKM values from normalized RNA-Seq data?

I know that the discrete raw counts from the RNA-Seq data are usually modeled by a negative binomial or a Poisson distribution, but what I am working on are the FPKM (Fragments Per Kilobase of ...
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180 views

Differences between TM and GDT-TS scores for structure comparison [closed]

What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
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4answers
8k views

How to calculate p-values for fold changes?

I'm currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups ...
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0answers
67 views

ngs time course experiment [duplicate]

I have a question regarding the RNA-Seq analysis. We have a time course data regarding a mouse model wt and mutant treated with a drug (10uM) and the taken down at different time points: 8 time ...
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1answer
366 views

When performing differential expression analysis, should genes with low read counts be removed before or after normalization?

I have RNA seq data which I've quantified using Kallisto. I'd like to use tximport to transform the read count data into input for EdgeR, following the R code supplied in the tximport documentation: ...
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2answers
1k views

How can I use Arlequin via the command line?

I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin ...
3
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1answer
39 views

How does Cellminer's "Cross-correlations of transcripts, drugs, and microRNAs" work

I have seen one of Cellminer tools. I am not sure how do they calculate the cross correlation of the genes, what does it actually mean? Based on what databases? For example if I take their example ...
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676 views

Difference between computational biology, bioinformatics and biostatistics [closed]

I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...
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2answers
262 views

How to calculate statistical significance of sequence motifs

I would like to show that certain types of RBP motifs are enriched in RNA editing islands (i.e. clusters of RNA editing). However, I am unsure about how to think about sequence motifs with respect to ...
6
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1answer
2k views

How to select a power for a scale-free topology network

In a weighted gene co-expression network analysis (using WGCNA), the soft-threshold power is recommended as a noise filtering. It consists on raising the correlation to a certain number. To decide ...
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1answer
135 views

Expected allele frequency distribution of SNVs in real NGS data

I have a huge amount of ~20x human WGS samples, aligned, and all SNVs that were called with GATK under standard germline parameters set. What I need to do is to model SNVs Allele Frequency (AF) for ...
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4answers
216 views

How to correlate two zero inflated bedgraph-like signals?

This question pertains to iCLIP, but it could just as easily be ChIP-seq or ATAC-seq or mutation frequencies. I have iCLIP read counts across the transcriptome and I wish to know if the signals are ...

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