Questions tagged [gse]

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1 answer

Error downloading GSE dataset

I've installed GEOquery with install.packages("BiocManager") BiocManager::install("GEOquery") library(GEOquery) then I ran the command ...
1 vote
1 answer

GEOquery errors due to list input

I want to extract the expression matrix from the GSE object in GEOquery. ...
4 votes
1 answer

How to extract gene expression tables from this GEO dataset?

I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene ...
3 votes
1 answer

Integration of different microarray dataset to run GSEA

I'm planning to run a GSE Analysis on some microarray datasets. Until now what I have done is to pre-processed them using frma algorithm. The reason I chose frma instead of gcrma or rma is that I ...
6 votes
1 answer

Gene set enrichment analysis on differential phosphorylation sites

I have: A list of differentially phosphorylated sites in a knockout condition. Some genes contain as many as 70 possible phosphorylation sites; others contain only one. A list of genes belonging to a ...
13 votes
2 answers

Are fgsea and Broad Institute GSEA equivalent?

Several gene set enrichment methods are available, the most famous/popular is the Broad Institute tool. Many other tools are available (See for example the biocView of GSE which list 82 different ...