Questions tagged [p-values]

Relates to the probaility of an observation being correct, usuaully considered significant at a threshold of 5%

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

Typically, a p-value of $p<=5*10^{-8}$ is used for genome-wide association testing, as there are roughly $1/p$ independent LD blocks in the human genome, so it correct for multiple testing across ...
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0 votes
1 answer
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What is the best way to compare treated/control samples? [closed]

I have two populations of mice, say RED and GREEN; there are 5 pairs treatment/control in each. The table is the following: ...
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How should I use FDR p-value correction in case of multiple subject with multiple parameters?

In my experiment I have 45 subject. On each subject we measured two set of paramaters. Set A contains 23 and set B contains 203 unique parameter. I use spearmann correlation test to find connenction ...
-1 votes
1 answer
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Adjusted P-value from DESeq2

What does the padj really mean? I believe it's a BH method, where it attempts to quantify the likelihood of a "false positive" but I am not sure. Also, what does it mean if the resulting ...
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1 vote
2 answers
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P value recalculation from multiple analysis (Transcriptomics)

I've done a differential expression analysis with transcriptomic information (microarrays and RNAseq) from different datasets by applying for some of them t-test and for the rest Wald-test. I've got ...
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0 votes
1 answer
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How to compute a p-value for the similarity measurement of two DNA sequences/contigs?

I'm attempting to come up with a statistical model to determine the p-value for the similarity value $ 0 \le s \le 1 $ of two DNA contigs. The idea is to get a numerical measure to estimate if two ...
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2 votes
1 answer
101 views

How does FDRtool work?

I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired using Deseq2), the FDRtool was first used and thereafter p.adjust using the benjamini hochberg ...
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3 votes
2 answers
591 views

Extracting p-values using corrr package in R

I'm performing correlation analysis using the corrr package in R, but I'm unable to extract the p values. Does anyone know how to get the p values in corrr package in R?
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0 votes
1 answer
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Odds ratio and enrichment of SNPs in gene regions?

I did a QTL analysis with a panel of 7M SNPs, and want to analyze the enrichment of the significant qtl-SNPs in different genic regions (promoters, gene bodies, TFBS, etc.). A straightforward way to ...
1 vote
1 answer
909 views

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one ...
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1 answer
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P-value correction when evaluating correlation between gene and miRNA expression

First of all I apologize without the question is very basic, I am taking my first steps in bioinformatics. Data information We are evaluating the correlation (using the Pearson, Kendall or Spearman ...
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0 votes
1 answer
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how can i calculate p value of miRNA raw reads counts using R?

working on lung cancer project and need to find out which genes are deferentially expressed and which are not. for that i a have downloaded miRNA data set from GEO id is GSE110907. And the file i got ...
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2 votes
2 answers
95 views

Difference between clinical significance and statistical significance

I am working on a clinical data analysis project and am from IT domain. While I am analyzing the data, I came to know that though some of the variables are not statistically significant, they are ...
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2 votes
2 answers
658 views

Strange p-value histogram for differential gene expression analysis

I'm trying to perform pretty standard differential expression analysis using RNA-seq data. I've used Kallisto to perform RNA quantification and am using Sleuth to perform the differential expression ...
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