Hey all, I am wondering what's the difference between getGEO and getGEOSuppFiles. I know that getGEOSuppFiles gets the supplemantary file in the GEO and getGEO is for retrieving the SOFT format but I do not know what is the difference in terms of data. Is the data in SOFT fromat processed? Thanks

When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use getGEO you get the processed data (and how they processed the data is supposed to be included in the submission, so you can look it up to see), and when you use getGEOSuppFiles, you download the raw data, if available. For RNA-Seq submissions if you want the FASTQ or SRA file, you can either use functions in the SRAdb package, or just get the SRA toolkit from NCBI and use fasterq-dump at a terminal prompt.