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Questions tagged [q-value]

Statistics: Also known as False discovery rate

Statistics: Also known as False discovery rate

15 questions
32
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5 answers

Calculating adjusted p-values in Python

So, I've been spending some time looking for a way to get adjusted p-values (aka corrected p-values, q-values, FDR) in Python, but I haven't really found anything. There's the R function p.adjust, but I would like to stick to Python coding, if…
erikfas
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2 answers

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
2
votes
1 answer

How to add a q value (adjusted p-value) to a modelsummary table after pooling the results of a multinomial model over multiple imputed datasets

I am using modelsummary to display the results of several multinomial models, each pooled over 5 datasets using the mice::pool function. It works great, but I want to add the q-value / adjusted p-value for false discovery rate. I understand I need…
Alex
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0 answers

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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0 answers

Package "jaccard" not installing properly

here is the code I am using: install.packages("jaccard") library("jaccard") The error code I receive is: Error: package or namespace load failed for ‘jaccard’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no…
JessieElliott
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2 answers

Implementing Q-Value Iteration from scratch

I am taking an online course, where I came across submitting many Q-Values. So, I wrote a Python script to calculate it automatically. I have used the following equations. But the script is not performing as it should. Its giving wrong…
Ashutosh Agrahari
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0 answers

Error in smooth.spline(lambda, pi0, df = smooth.df) : in qvalue package

I have 1493313 p values in a data frame: > head(dt) pvals 1 0.0084956486 2 0.0012681537 3 0.0021218873 4 0.0001551133 5 0.0001894240 I am trying to use qvalue package to calculate True Positive Rate. (TPR) I am doing this and getting…
anamaria
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ggplot2 and qvalue error: Don't know how to automatically pick scale for object of type qvalue

I have a data frame consisting of 1893 p-values that I convert to qvalues using the R package qvalue: pvals <- read.table("p_values.csv",header=T,sep=",",dec=".") The qvalue manual states you can directly plot (using the qplot function) the output…
sk1985
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1
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1 answer

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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1 answer

R: Using Qvalue, how do I find the number of SNPS that have FDR adjusted p-values of p<.05?

I want to find the number of SNPS that have FDR adjusted p-values of p<.05. However, my for loop and if statement did not effectively find the # of SNPs with p<.05. My dataset has a P column which indicates p-value and 1422 observations. >…
melolili
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0
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1 answer

P vs Q values in the proteomics experiment

I have a question regarding the p and q values that I observe in my statistics of analysing protein expression. I get the following p values that are very significant, however the Q values are very high. I have performed this analysis in a Software…
Matiss Ozols
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0
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0 answers

Volcano Plot Error......... "Error in FUN(X[[i]], ...) : object 'Qval' not found"

I'm getting quite confused when I'm doing my using the ggplot function. When I input the following code with ggplot: I actually get the volcano plot and don't receive an error ##--> Add the pval and the qval average_data$Pval <-…
ww22an
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limma: Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed

I have one dataset for comparing the control and treatment and use limma for the pval. It worked well with most of my data untile I got one like this. I can tell there are differences between control and treatment. But I got error: " Error in…
L.C
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How to calculate True positive rate in R?

I tried using qvalue function to calculate TPR: library(qvalue) qval_obj=qvalue(pvalR) pi1=1-qval_obj$pi0 but after running: qval_obj=qvalue(pvalR) Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are…
user2458189
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0 answers

How convert q-value to p-value?

I have a vector as below , I like to convert q-value to p-value (estimate p-value base on q-value). data<-c(0.35,0.52,0.12,0.46) I used below code for converting but I am not sure about it:(I take this code from here…
star
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