How to extract gene list from GEO dataset in R

Question

[decorus]

Hi,

I'm new to bioinformatics and I've been trying to analyses some studies and I've been using the GEO2R function on the GEO repository, but some studies I wanted to use don't have GEO2R analysis enabled so I have to do it manually through r studio. Can anyone set me up with a walk through of how to do this. I have been able to download the series matrix file into r studio but i get error messages when i try do more steps. Any help is appreciated, the set I'm using is GSE239903 if that helps

(for further context ive installed "GEOquery", "limma", "Biobase", and have uploaded the study but am not sure where to go from there. I'm just trying to get the gene lists & log2fc)

[manaswwm]

What type of error are you getting? How does the series matrix file look like?

[Shohel]

Hi I saw the GSE239903 dataset. It contains RNAseq data along with ATACseq data. To get the gene IDs you can follow the scRNA seq pipeline which can be done through Linux operating system. You have to just work with one sample with the help of reference genome. Then you can get all the gene IDs with their characteristics.