I performed transfection with viral replicons, and control as mock and non-replicating viral replicon genome. The data are from three independent biological repeats, so there are some variance. Each of the repeats seems located in one area. So I wonder whether a bulk RNA-Seq batch correction would help.
Code should be placed in three backticks as shown below library("DESeq2") library("ggplot2") library("pheatmap")
setwd("~/rnaseq") countData <- read.csv('counts.mm39_reduced.csv', header = TRUE, sep = ",")
metaData <- read.csv('metadata_separate.csv', header = TRUE, sep = ",")
dds_data <- DESeqDataSetFromMatrix(countData=countData, colData=metaData, design = ~ condition, tidy=TRUE)
dds <- DESeq(dds_data)
resultsNames(dds)
vsd <- vst(dds)
pca <- plotPCA(vsd, intgroup="repeat")
include your problematic code here with any corresponding output
please also include the results of running the following in an R session
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