DeSEQ2 analysis

[Coolaline13]

Hi,
I am having trouble taking the excel spreadsheet of raw counts that are ordered by genes(row) and treatment condition and replicate(column). I want to run it through Deseq2 to get a normalized matrix file that I can then run through gene ontology. If you have any suggestions or ideas pls let me know.

Thank you guys,
Gabriel Viramontes

[DavoWW]

Hi @Coolaline13,
Its not clear from your question how far you have got through this process. Also, remember that R is case-sensitive - I have assumed you want to use the DESeq2 BioConductor package. If so, I think you will need to do something like this:

install.packages(BiocManager)
library(BiocManager)

BiocManager::install("DESeq2")
library(DESeq2)
help("DESeq2-package")

# Read your data file (give your first column a name e.g. "gene")
library(readxl)
your_data <- read_excel(path="your_Excel_file_name", sheet="Sheet1", col_names=TRUE)

# Manipulate your data into the format that DESeq2 requires (a matrix)
library(tidyverse)

your_matrix <- as.matrix(your_data[, c(2:5)])

# Modifying code from help examples
condition <- factor(c("Treatment","Treatment","Control","Control")
dds <- DESeqDataSetFromMatrix(your_matrix, DataFrame(condition), ~ condition)
DESeq(dds)

HTH