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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SKAT method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
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Simes method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
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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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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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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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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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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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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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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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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 ...
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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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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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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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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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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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