Hi, I'd like to perform GSEA for glioblastoma multiforme samples to analyze immune cells infiltration. What kind of data do I need (RNa-Seq, microarray)? Is it possible to download them from TCGA data portal? Sorry but I'm complete beginner...
Either RNA-Seq or microarray gene expression platforms could be used. In theory, so could methylation platforms.
If you are analyzing bulk samples (and I guess from your question that you are), you might want to check out xCell, CIBERSORT and other cell proportion estimation methods. I think there are lots out there.
These attempt to deconvolute the gene expression vector for each sample to infer the proportions of various cell types. Immune cells are supported by both of the methods I linked to. xCell already has pre-computed TCGA cell type proportion estimates available to download, so there's no need to run anything.
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Thanks, but can I download those data from TCGA? How dhould they be processed?
See the https://portal.gdc.cancer.gov/repository for the location of the data files. If in asking "how should they be processed" you are asking how to "perform GSEA for...immune cells infiltration", this is an area of active research and is not a solved problem. A review of the literature is really going to be necessary, I suspect.