5 votes

Extracting p-values using corrr package in R

I would suggest looking at some of the documentation. As far as I can tell, the intention of the package is to visualize and organize correlation coefficient estimates. It does not seem that the ...
Maximilian Press's user avatar
3 votes
Accepted

Odds ratio and enrichment of SNPs in gene regions?

The first approach only address the question of how likely are you to end up with the observed over-representation given the MAF distribution. My suggestion is to use the second approach, but I am not ...
StupidWolf's user avatar
  • 1,678
3 votes

What is the best way to compare treated/control samples?

I don't really understand the table, particularly the 'p-value' in the header. More generally I don't really understand the experiment nor the data. As a general rule the Wilcoxon would be a ...
M__'s user avatar
  • 11.9k
3 votes

Difference between clinical significance and statistical significance

This is non-parametric statistics, the mean requires confirmation to the normal distribution (but there are exceptions), or perhaps better put it requires a fixed relationship between mean and ...
M__'s user avatar
  • 11.9k
2 votes
Accepted

Difference between clinical significance and statistical significance

Another viewpoint could be : statistically significant implies use of sampling theory to establish presence of significant difference between case and control groups. The "clinical " significance ...
Subhash C. Davar's user avatar
1 vote

Why is the p-value significance threshold for HLA association tests $5*10^{-8}$?

As a direct answer to your question, I would argue that the authors, in choosing this threshold, have demonstrated a lack of understanding of their process of analysis. But that answer is not a full ...
gringer's user avatar
  • 13.8k
1 vote

Why is the p-value significance threshold for HLA association tests $5*10^{-8}$?

Its a very good question and it is also a good study. What you are saying must be correct. I thought it was possible they used the correct critical probability in the original submission and a ...
M__'s user avatar
  • 11.9k
1 vote
Accepted

Strange p-value histogram for differential gene expression analysis

I found that using the Wald test instead of the Likelihood Ratio Test produced very different results with respect to the p-values. ...
James Hawley's user avatar
  • 1,374
1 vote

Strange p-value histogram for differential gene expression analysis

Try the protocol here for generating a different (smaller) dispersion estimate https://www.huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#inspection-and-correction-of-pvalues
swbarnes2's user avatar
  • 1,882
1 vote

Adjusted P-value from DESeq2

If we look at documentation of DESEQ2 and search "adjusted p-value", we find the section "Multiple test correction". In this section they discuss Benjamini-Hochberg ("BH")...
Maximilian Press's user avatar
1 vote

How to compute a p-value for the similarity measurement of two DNA sequences/contigs?

Well, here my thoughts: The equation $s$ somehow tries to represent the ratio $\frac{equality}{equality+inequality}$. But $s$ returns only a value. And to assing the p-value to a single value... is ...
Ivan Castro's user avatar
1 vote

How does FDRtool work?

Something like this book chapter might help on understanding FDR. The packages or functions you call differ in their estimation of pi0 or the proportion of null hypothesis. Basically, the ...
StupidWolf's user avatar
  • 1,678
1 vote

Extracting p-values using corrr package in R

Here is a suggested workaround: Generate a p-value table using one of these tools: RcmdrMisc::rcorr.adjust() psych::corr.test()...
Tripartio's user avatar
  • 111
1 vote

Seurat FindMarkers() output interpretation

The p-values are not very very significant, so the adj. p-value. You need to plot the gene counts and see why it is the case. It could be because they are captured/expressed only in very very few ...
geek_y's user avatar
  • 321
1 vote

how can i calculate p value of miRNA raw reads counts using R?

I would start by re-formulating the question in this post: Your end-goal seems to the differential expression analysis (DEA) of your samples (and you have to have to levels for this like treatment-...
haci's user avatar
  • 3,947

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