Could anyone help me get some sort of a count matrix when processed RNA-seq data is extracted from GEO. I have some experience using microarray data from GEO.
For example, for GSE78220, the data has been processed by: "FASTQ files were mapped by Tophat2 Tophat BAMs were quantified and normalized using Cuffnorm (for gene analysis) and by htseq-count followed by edgeR's log CPM (for gene-set analysis) Genome_build: hg19 Supplementary_files_format_and_content: The normalized expression levels by cuffnorm"
After geting the GSE by:
g <- getGEO("GSE78220")
What would be the next step?