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Questions tagged [fdr]

FDR is a tool for analyzing programs written in Hoare’s CSP notation.

FDR is a refinement checker for the process algebra CSP. It allows processes to be defined in a machine-readable version of CSP, CSPM, and is then able to check various assertions about these processes. FDR includes two main tools.

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How Does R Calculate the False Discovery Rate

I appear to be getting inconsistent results when I use R's p.adjust function to calculate the False Discovery Rate. Based upon the paper cited in the documentation the adjusted p value should be calculated like this: adjusted_p_at_index_i=…
JGibbRandomNumber
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FDR4.2.7 could not connect license server

I need to use FDR4 for my papers，but when I download FDR4.2.7, I find I could not connet to the licensing servers. I also see the FDR release note: Release Notes 4.2.7 (11/05/2020) Fixes an additional issue that meant FDR4 could not connect to the…
user14112451
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How to add adjusted pvalue to the corrplot matrix?

I used following code to create correlation matrix and generate pvalue. How do I create adjusted pvalue for each correlation? library(corrplot) #Running correlation M = cor(mtcars) #identifying pvalues testRes = cor.mtest(mtcars, conf.level =…
user2110417
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Welch t-test, adjust p-value on permutation based FDR in R

I would need some help to find a way to compute q-values from Welch p-values in R, using permutation FDR method, as for SAM technique. Assuming my data are as follow x = matrix(rnorm(1000*3),nrow=1000) y = matrix(rnorm(1000*3),nrow=1000) I can…
pisistrato
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R 'fdrtool' package: how to use t statistic

Can one use t statistics from a Student's t-test directly in the fdrtool() function of fdrtool package (ver. 1.2.12)? The paper (Strimmer-K BMC Bioinfo. 2008, 9:303) mentions this but as far as I can see the parameters only recognize "normal",…
user3375672
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How to find value that corresponds to FDR=0.05 given distribution A and a null distribution?

I have two vectors of correlations: one which represents real correlations, and the other permuted correlations (the null distribution). I want to find the correlation value that corresponds to a FDR of 0.05. Updated…
Rebecca Eliscu
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FDR correction - extracting p-values from lmer() and creating vectors for use in p.adjust in R

I am trying to do FDR correction for some region of interest neuroimaging data. I have run 18 linear mixed effects models overall and I have made sure that the order of the coefficients in the output would be the same in each model. I have saved the…
Monika Grigorova
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Adjust significance levels for multiple testing in correlation plots

I'd like to adjust for multiple testing when plotting multiple correlation tests. corr.test from the psych package works well, but doesn't have a nice graphical output. I'm particularly interested in using ggpairs from the GGally package because it…
RLB
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How to declare a data-contructor with same name but different type in CSPm(Communication Sequential Process)

I am learning to model check the security protocol by using CSPm and FDR I start it from implementing an early paper: Breaking and fixing the Needham-Schroeder Public-Key Protocol using FDR, Gavin Lowe, TACAS 1996 This is my code snippet: -- NSPK…
Tool Ply
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How to calculate and add an FDR column to file in python

I have the following input file (Input.xls): Mouse No_neigh_mouse Human No_neigh_hum Intersection TotalGeneTested Gm20645 1 lnc3 2 1 8 Gm20645 1 lnc2 1 0 8 Gm20645 1 lnc1 2 1 8 Gm26549 2 lnc3 2 1 …
BioProgram
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How to avoid deadlock in processes executing in parallel through addition of another process in CSP

PC1 and PC2 run in parallel with the same alphabet. They deadlock. I want to find a process (alphabet as yet undefined) which I can run in parallel with PC1 and PC2 which will solve the deadlock issue. Any ideas? Regards. This is my code file so…
Danny Rancher
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FDR of comparing two vectors

We are given a matrix with 2 columns (samples, experiment conditions) and n rows (genes for example), and we aim to identify the genes that have significantly changed (at a specific FDR) between the two samples. How to perform this using R? Below…
Ali
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Using a temporal inner variable in dplyr outside of the group

I need to calculate an FDR variable per group, using an expected random distribution of p values (corresponds to the "Random" type). library(dplyr) library(data.table) calculate_empirical_fdr = function(control_pVal, test_pVal) { m_control =…
lizaveta
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FDR of neuroimaging data with Statsmodels: many of the corrected p-values have the same value

I ran a number of Pearson's R correlations and I then wanted to correct for multiple comparisons using Statsmodels. Specifically, I used this function. Given a list of p-values, the function returns whether the hypothesis was rejected or not, based…
Davide
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Apply FDR correction on a large number of outcome variables

I'm using R (not the 4 version yet ahah) I was advised to use FDR correction on my linear models. I have >200 participants, 140 continuous outcome variables, and each outcome variable is tested on the same 4 predictors. So all the models are: Y ~ x1…
WannabeGandalf
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