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How to perform paired t-test in R for obtaining p-value of each gene?

I'm interested in paired t-test for obtaining p-values for each gene. I used the t.test function in R, but it only gives one single p-value. How do I get p-value for all genes? I have 46 pairs of tumor and normal samples.

####Load necessary packages######

library(NOISeq)
library(edgeR)
library(DESeq2)
library(stats)
library(limma)
library(Rsamtools)

####Load the data #####

LIMS <- read.delim(file.choose(), row.names=1)

#####Perform paired t-test between tumor and normal samples####

Tumor <- unlist(LIMS[, 1:46])
Normal <- unlist(LIMS[, 47:92])
y <- t.test(Tumor, Normal, paired = TRUE)
p-value rna-seq z-score t-test
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updated by Ram Ram • written by prithvi.mastermind • prithvi.mastermind

I think you would need to run a 2-way ANOVA to get p-values for all genes. However, it's my understanding that false discovery rate (FDR) is the gold standard for RNA-seq.

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written by Jeremy • Jeremy

Following the DESeq2 pipeline, you directly get the adjusted p-values for all genes.

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written by Marco Pannone • Marco Pannone

Actually all my samples are paired and hence I want to apply paired t-test. I guess DESeq2 only offers unpaired two-sample t-test and not paired t-test.

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written by prithvi.mastermind • prithvi.mastermind

Want to make sure you saw ATpoint's post. You would include that information into the design by adding another column to your colData

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written by Trivas • Trivas

2 answers

You have to include the pairing information into the design, then you get a proper paired test in DESeq2. It’s a FAQ, see http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#can-i-use-deseq2-to-analyze-paired-samples

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written by ATpoint ATpoint

You already computed genewise paired t-tests using limma a few days ago: How to apply two tailed paired t-test in limma for DEGs selection?

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written by Gordon Smyth Gordon Smyth

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