how to create -gct and .cls files from RNASeq counts?
This is probably a stupid question but I really can not find an answer... I want to compare two DEGs sets from two different experimental settings in order to create a 'common DEGs set' and I found out that GSEA is a good way to do it but I need two types of files .gct and .cls
How do I create this files using my counts matrix that I was using for DESeq2? I found this https://rdrr.io/bioc/ArrayTools/man/output.cls.html but I am not sure what 'variable of interest' means and how exactly should I use this function (and similarly output.gct().
Or is it ok to just plot the Venn diagram for the two lists of DEGs? I am a bit lost after reading and searching....
• 3,313 views
•
link
updated
by
Ram
•
written
by
annamariabugaj •
•
written
by
annamariabugaj •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Trouble running GSEA analysis on log2 fold change values of RNA-seq data
written by trkfs •
-
WGCNA Error in moduleEigengenes: object 'trapErrors' not found
written by annamariabugaj •
-
Creating a cls file from two groups of TCGA RNA-seq samples
written by ivykosater •
-
vcf-compare and making Venn diagram
written by arshad1292 •
-
venn diagram of rna seq and microarray datasets
written by M.Mohareb •
-
Venn Diagram from count species in R
written by SergFly •
-
Create a Venn diagram for 5 VCF Files (each VCF file is a population)
written by mostafarafiepour
-
Venn diagrams for multiple (8) data lists in R
written by arronar
-
Venn diagram for vcf files
written by sukesh1411 •
-
Venn Diagram Help
written by kevluv93
I think you should read first what GSEA is actually doing. It is not giving you a common set of genes but will tell you if your DEGs will be signifiantly enriched (in either direction, up, down) compared to a set of genes (typically curated sets of genes e.g. from MSigDB).