Question: Gene Set Enrichment Analysis after DESeq2
1
gravatar for Sreeraj Thamban
6 months ago by
Indian Institute of Science Education and Research
Sreeraj Thamban90 wrote:

Hello Biostars, Can anyone tell me how to prepare input data set for GSEA after Differential Gene Expression Analysis by DESeq2? How will I rank the genes? Should I rank based on log2FC or Adjusted P value? Is there any way to generate a GSEA ready data directly from DESeq2?. I was using topGo for gene ontology enrichment analysis before and recently came across GSEA. Which one is better GO enrichment analysis or GSEA? Even after going through the papers I couldn't find a significant difference between above two.

Thank you

gsea rna-seq deseq2 geneontology • 1.3k views
ADD COMMENTlink modified 6 months ago by prakash100 • written 6 months ago by Sreeraj Thamban90
3
gravatar for prakash
6 months ago by
prakash100
prakash100 wrote:

Hi Sreeraj

Genes can be ranked based on fold change and P value and that can be used in GSEA package.

you can use this R code for this purpose.

x <- read.table("DE_genes.txt",sep = "\t",header = T)
head(x)
x$fcsign <- sign(x$log2.fold_change.)
x$logP=-log10(x$p_value)
x$metric= x$logP/x$fcsign
y<-x[,c("Gene", "metric")]
head(y)
write.table(y,file="DE_genes.rnk",quote=F,sep="\t",row.names=F)
ADD COMMENTlink modified 6 months ago • written 6 months ago by prakash100
1

in this case, what parameter should we input into GSEA?

ADD REPLYlink written 3 months ago by langya20
2
gravatar for Michael Love
6 months ago by
Michael Love1.6k
United States
Michael Love1.6k wrote:

Here's a link to an answer I wrote a few years ago for using the gene set testing package goseq following DESeq2:

https://support.bioconductor.org/p/64811/#64815

I'm not sure what kind of input GSEA takes. I also like the methods behind ROAST and CAMERA from the limma package, but I haven't yet worked on integrating with those methods. For those two, you would need to run a limma analysis upstream.

ADD COMMENTlink written 6 months ago by Michael Love1.6k

Hey I noticed in the newest DESeq2 version, the default setting of fold change is not shrunken fold change, may I ask why? i thought the shrunken fold change gives you higher confidence.

ADD REPLYlink written 27 days ago by langya20
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