6 votes
Accepted

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

The more genes you have the more robust the scaling factor is (among the reason why one doesn't normalize to ERCC spike-ins without a compelling reason), so I suppose in theory it's better to filter ...
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  • 19.2k
6 votes

What will be an appropriate mathematical distribution for SNP data?

Simulating genotypes with realistic correlation structures is indeed not so simple, and there's quite a few papers dedicated entirely to that (e.g. https://bmcgenet.biomedcentral.com/articles/10.1186/...
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  • 463
5 votes

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

FPKM/TPM values are generally log-normally distributed. Reference : Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
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5 votes
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LRT or LRT-like test on cyclical (Sleep) data

I think the problem is that you have time as a linear value rather than a factor. While this naively makes sense (after all, you have to go through 3 hours awake ...
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5 votes

Is it possible to do this in R?

R supports logistic regression, which would seem to be the most efficient method for tackling this question. Assuming the "Chemo" variable is the type of chemo the code would be something like: <...
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  • 151
5 votes

Economist article on coronavirus

R is a reference to R0, otherwise known as the basic reproductive rate, and means the number of new cases from a single patient infection. R0 has to be above 1 for a disease to persist. It is a ...
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  • 7,284
4 votes

Expected allele frequency distribution of SNVs in real NGS data

I don't have enough experience to answer which probabilistic distribution should be used. However, this questions also also asks how to estimate parameters of the distributions. If a binomial ...
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  • 2,051
4 votes
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How to calculate statistical significance of sequence motifs

As far as I remember the exact probability computation is an open problem. The reason is that potential motifs can overlap, which makes probability computations for an arbitrary string non-trivial, ...
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4 votes

How to correlate two zero inflated bedgraph-like signals?

Honestly I'd just use multiBigwigSummary and then plotCorrelation from deepTools for this, but I'm a bit biased. There, the idea ...
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4 votes

Matlab scatter diagram

A reverse image search on google leads to the exact code used to produce the second image: ...
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  • 1,806
4 votes

Comparison of gene set enrichment statistics

I assume that you are talking about the implementation of these methods in the limma package. Otherwise this answer does not apply. I think that your questions can be answered with some simulations ...
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  • 4,602
4 votes

Intuitive explanation of GSVA analysis

The most intuitive explanation is also explained in the background section: Conceptually, this methodology can be understood as a change in coordinate systems for gene expression data, from genes ...
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  • 4,602
4 votes
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Should PCA be standardized for gene expression?

When the gene expression is scaled and centred you reduce the difference between genes. Imagine you have one gene A that is highly expressed usually and has a standard deviation of 500 units ...
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  • 4,602
4 votes
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3D PCA group labelling

You can easily color 3D pca plots in R based on the code given below: ...
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4 votes
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Create a Grouped Barchart

I have noticed a few errors: 1) You define a bunch of variables (Species, Class, ...) but then instead of creating your data frame data with these you create it by reading from text. I don't think ...
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  • 3,432
4 votes

Is it possible to do this in R?

The general approach would be to loop through every column starting at column 2. You can use numeric indexes to do that. For each column, check its type. If it is a factor, use your ...
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  • 1,370
4 votes
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Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?

This may not strike most as a bioinformatics, but getting the key clinical outcome is essential in understanding the molecular basis of pathogenicity. I think the mortality rate is over-reported. ...
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  • 7,284
4 votes
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Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)

There is no such thing as a hypergeometric test, at least in statistical textbooks. It's a fisher test based on hypergeometric distribution. If it is chip-seq for the same target, i.e biological ...
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  • 1,628
4 votes
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Inflated p-values in quantitative trait analysis

Permutation as suggested by @StupidWolf's comment is essential to understand what's going on. If permutation makes this pattern go away, then you have a problem with your model specification, there's ...
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4 votes
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What does aov(glm model) actually do in R?

It's not appropriate to run aov on a GLM model. aov assumes normally distributed data and it runs on a GLM as if it was a least ...
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3 votes
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Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

...
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  • 19.2k
3 votes
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Standard Cutoff for Moderated T-statistics

You're misinterpreting the moderated T-statistic, it's basically the fold-change divided by its variance. The p-value comes directly from that, so if you filter by moderated fold-change you're just ...
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3 votes

How to calculate p-values for fold changes?

Your null hypothesis would be that the fold-changes are 0, so you can either do the T-test accordingly or simply do away with the fold changes and perform the T-test between the raw values in the ...
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  • 19.2k
3 votes

How to calculate p-values for fold changes?

The key point here is whether or not the values are approximately normally distributed and whether any transformations can be applied to make them so. For a t-test, the most important thing is that ...
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3 votes
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How can I use Arlequin via the command line?

For MAC OSX, the executable found in arlsumstat_macosx (arlsumstatmac_64bit) seem to work appropriately. The directory for ...
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  • 203
3 votes

How to correlate two zero inflated bedgraph-like signals?

It depends whether you want to treat the peak intensities as binary (comparing presence/absence of peaks in the sets) or continuous (comparing the relative magnitudes of the peaks). Binary For ...
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3 votes

How to correlate two zero inflated bedgraph-like signals?

Rather than working on the base level, you could probably work on say gene level counts. Kendall's tau, an ordinal association metric, can then be used as an appropriate correlation measure. If $X$ ...
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3 votes
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Understanding PCHeatmap outputs

The PCHeatmap function (renamed DimHeatmap in Seurat v3) can be used to help determine the number of principal components to use ...
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  • 674
3 votes

Economist article on coronavirus

R, the reproductive number, relates to the average number of (new) people that will get sick (infected) per person that is already sick. For instance, if $R=2$ and you start with a single infected ...
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3 votes
Accepted

When should I apply a multiple comparison adjustment?

The p-value adjustments corrects the inflated number of significant results when performing many significance tests. If you have a test with 5 % false positive rate and but you run it several times ...
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