After a lengthy struggle (I am a beginning student), I was able extract a list of genes from one GSE which contained 25 GSMs. From this GSE, I extracted a list of gene symbols after which I removed all of the duplicates. So, I am now assuming that the gene symbols I obtained are from all of the GSMs within that GSE? If so, I am attempting to perform the same operation on six additional GSEs before removing duplicates and using the RobustRankAggreg package, aggregating all of the genes into one data object (vector?) before performing a differential expression analysis with the limma package to isolate a smaller set of DEGs that I could use with Cytoscape via RCy3. Unfortunately, I don't know how to retrieve genes from multiple GSE objects or how one would combine all of the gene symbols. Can limma accept one monolithic data structure of gene symbols and could a boxplot be constructed from it even though there would presumably need to be two categories? Please accept my apologies if any of the above text is incorrect. I am working on my own without any form of guidance from my PI, TA, or classmates. I am, however, finding the limma course from DataCamp to be quite useful.
Code should be placed in three backticks as shown below
library(GEOquery) library(limma) gse <- getGEO("GSE12657", AnnotGPL = TRUE) features <- fData(gse[]) View(features) length(features$`Gene symbol`) # Remove duplicates leaving 9156 unique genes features <- features[!duplicated(features$`Gene symbol`),] # include your problematic code here with any corresponding output # please also include the results of running the following in an R session sessionInfo( )