normalization using Deseq2
1
0
Entering edit mode
@11819287
Last seen 5 days ago
Pakistan

i have normalized the data using deseq2 internal normalization method. But it seems that my original input data is same as the normalized output. i don't know if the data has been normalized correctly or if there is any issue with my code. Because when i am going with the current normalized data it is giving me a very few up and down regulated genes on adjusted p value <0.1

Code should be placed in three backticks as shown below


library(DESeq2)
library(tidyverse)
count_data <- read.csv('rawcount_data2.csv',row.names = 1)
head(count_data)
colData <- read.csv('rawdatainfo.csv', row.names =1)
all(colnames(count_data) %in% rownames(colData))
all(colnames(count_data)== rownames(colData))

dds <- DESeqDataSetFromMatrix(countData = count_data,
                              colData = colData,
                              design = ~ condition)
levels(dds$condition)
dds
keep <- rowSums(counts(dds)) >=10
dds <- dds[keep,]

dds
#dds$condition <- relevel(dds$condition, ref = "healthy")

dds <- DESeq(dds)
# Get the normalized counts
normalized_counts <- assay(dds)

# Write the normalized counts to a CSV file
write.csv(normalized_counts, file = "normalized_counts3.csv")
res <- results(dds)
res

summary(res)

sessionInfo( )

the original data before normalization input raw data structure after nomaliztion the data looks like nomalized_counts structure

DESeq2 rnaseqGene Normalization • 111 views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.1k
@atpoint-13662
Last seen 10 hours ago
Germany
counts(dds, normalized=TRUE)
ADD COMMENT

Login before adding your answer.

Traffic: 493 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