Gene Set Enrichment Analysis after DESeq2

Question: Gene Set Enrichment Analysis after DESeq2

3.3 years ago by

Indian Institute of Science Education and Research

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 • 12k views

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modified 2.2 years ago by enxxx23 • 240 • written 3.3 years ago by Sreeraj Thamban • 220

I like DESeq2. It would be great to have in the future something like ROAST/CAMERA/GSEA in DESeq2 too!

ADD REPLY • link written 2.2 years ago by enxxx23 • 240

3.3 years ago by

Prakash • 2.1k

India

Prakash • 2.1k 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 COMMENT • link modified 3.3 years ago • written 3.3 years ago by Prakash • 2.1k

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

ADD REPLY • link written 3.1 years ago by langya • 90

How would you handle NA values?

ADD REPLY • link written 2.1 years ago by t-jim • 30

.....

filtered <- na.omit(y)

write.table(filtered ,file="DE_genes.rnk",quote=F,sep="\t",row.names=F)

ADD REPLY • link written 18 months ago by Barry Digby • 630

I have used this code but am struggling to obtain a table where the gene names are appearing as names and not numbers, for some reason it keeps saving a table with the ranks but no gene names.

ADD REPLY • link written 18 months ago by g.birch15 • 0

Try row.names = TRUE.

Also, you want to use col.names = FALSE, as GSEA complains when 'Gene' and 'metric' are in the rnk. file.

ADD REPLY • link written 18 months ago by Barry Digby • 630

3.3 years ago by

Michael Love • 2.1k

United States

Michael Love • 2.1k 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 COMMENT • link written 3.3 years ago by Michael Love • 2.1k

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 REPLY • link written 2.8 years ago by langya • 90

You can generate these via lfcShrink()

ADD REPLY • link written 3 months ago by Kevin Blighe ♦ 69k

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