I am new to both coding and GEO so this may be a silly question.
I need the raw_counts data set for the GEO data set I am using but data in the downloads box is not the raw_counts. How would I be able to find the raw counts?
As I am new to both I decided to use GEO2R to run an analysis and then to see if I could create the same results using code in R as I new that I could look at the R script for GEO2R if needed.
I was struggling with which of the files I needed to download so I looked at the R script used in GEO2R but the files that are being used are completely different to the ones that I have downloaded.
I am using the data set for Series GSE178646 "CRISPR gene editing and inducible pluripotent stem cell neuronal disease modelling for rare disease diagnosis: EMHM1 genetic variant analysis in Kleefstra Syndrome" and am only interested in CF7-12 but the files that I have downloaded are called
"GSM5395222_CF7_kallisto_abundance.tsv.gz" where as in the R script in GEO2R the code has used the file
"GSE178646_raw_counts_GRCh38.p13_NCBI.tsv.gz" and I am really not sure where I could access this file.