goseq code after DESeq2 -NO IDEA!
0
0
Entering edit mode
9.0 years ago
amyfm ▴ 10

Hi,

After DESeq2 analysis of my RNAseq data in order to obtain differentially expressed genes between 2 cell types, I have a csv file with approximately 26000 genes, of which around 6000 genes are differentially expressed (padjustedvalue < 0.05). Now I want to use goseq in order to study pathways.

I am a very amateur R user and I am starting to learn about all this, so I have no idea what I have to do now. By checking this website http://www.bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf, I understand that I have to create 2 vectors, one with all my genes, and other with the DEGs. After that, I get lost. What I have done until now in order to create the vectors is the following, although I am not sure if it is correct:

d <- read.csv("myfile.csv", header=T, row.names=1)
all_genes <- row.names(d)
DE_genes <- all_genes[which(d$padj<0.05)]
head(DE_genes)

I will really appreciate if someone can give me the scrips/code in order to do goseq analysis, starting from my file.csv with all the genes.

Thank you

deseq2 goseq • 3.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 1329 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