I am looking to download the 450k methylation data from this paper https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65820 on GEO and I'm using the minfi R package to analyse it.
Ideally I could access the processed (normalised, QC etc.) data but is it in a format that is compatible with minfi? (It seems like minfi needs an IDAT file and it is mentioned as being in the "sample table" but I'm not sure what or where that is). How would I go about downloading that instead of the raw idats from the .tar file and can I use this in minfi?
I want to download the data to a HPC. Is there a way to do this that preserves the sample ID? (AOCS_001, AOCS_4 etc.) rather than the plain GSM ids that are contained in the .tar file? How can I avoid individually matching up the AOCS id and the GSM ids?!
If you need to download the IDAT files then you can simply get the entire archive using: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE65820&format=file
@GenoMax Thanks! can I also get the processed data all together instead? and how can I get the sample names to match with the IDAT files?
I don't think they have provided processed data as a single upload.