bulk RNA-Seq batch correction
1
0
Entering edit mode
jg0428 • 0
@f4756730
Last seen 14 months ago
United States

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

```

RNASeqData rnaseqcomp RNASeq • 704 views
ADD COMMENT
1
Entering edit mode
ATpoint ★ 4.5k
@atpoint-13662
Last seen 5 hours ago
Germany

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

ADD COMMENT

Login before adding your answer.

Traffic: 617 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6