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

```

See the vignette on batch effects. For more details please show PCA plot and colData.