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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short Read/percentage threshold for bacterium presence in metagenome
I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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Normalization in Sequence Analysis Research
I am currently engaged in a research project that involves DNA sequence analysis, utilizing nanopore and KMA alignment software (k-mer alignment). As I delve deeper into my research, I am faced with a ...
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time*treatment series with repeated (i.e: NOT independent) sampling of replicates
I am performing the analysis of cell cultures in suspension, untreated(U) and treatment A and B, at t0, t1 and t2, 4 replicates per treatment.
The experiment started with 12 cultures, 4U, 4A and 4B, ...
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Is this the correct method for determining Power at a given alpha, VAF, and coverage threshold?
I'm trying to calculate power at a given VAF, target coverage, and alpha. For example, what would my power be for a 100x coverage site, detecting VAF of 0.10 with an alpha of 0.05. This is what I came ...
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permutation test in edgeR
I have a simple RNA-seq experiment with treatment and control, each with 3 biological repeats. I run my data through edgeR and obtained differentially expressed genes (DEGs). Due to the low sample ...
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SNP Signatures with Limited WGS Data:
On 80 WGS samples, I'm dissecting SNP signatures linked to milk production in a scarcely studied animal. Post-variant calling and QC association analysis have been tricky. I'm here to tap into our ...
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How to do post hoc comparisons after a repeated measures ANOVA in R
I have a data set of several samples with their expression of proteins, in response to four different doses of a drug and two genotypes. I have been able to generate the two-way ANOVA using ezANOVA ...
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Calculating Fisher's exact test for COG categories
This is a continuation of the following question -
Fisher's exact test for COG categories in pan, core genome analysis
Also, the dataset -
How do I perform a Fisher's exact test on this data to ...
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In medical and public health care, should we make use of "clinical" signficance testing (non-parametric tests) or parametric tests of significance?" [closed]
In certain cases, traditional significance test may not be able to identify that effect of a treatment or a drug is significant. However,clinical significance test may suggest a significant effect. ...
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limma linear model with interaction
I want to run some epigenome wide association studies based on city and pollutant type, could you please suggest if I can get DNA methylation sites (CpG) association based on pollutant type for each ...
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Fisher's exact test for COG categories in pan, core genome analysis
I have come across several papers that do a Fisher's exact test to show over represented genes in COG categories specifically in a pan-core-accessory-species specific genome analysis. The test is done ...
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probability of finding a 5 amino acids in a row within a proteome
How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues.
The probability of a ...
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Statistical approach to link DNA methylation with toxic element exposure and health outcome
I would be thankful to you if you can help with the statistical approach for case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
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Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?
Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
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Mendelian randomization
I would be thankful to you if you can help with how I can use MR from my case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
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