Note that '[[1]]' above -- gse.geo is a list and I never understood why, so I naively just took the first element. I still don't know why, though I suspect it may be that each list element corresponds to a different platform. e.g., the example above was data generated on both the HiSeq 2500 and NextSeq 500.
This is a larger issue beyond this one dataset and I'm not going to attempt to fix it now.
We are missing files from some GEO datasets. One example is GSE87517/PRJNA345006
https://staging.csbc-pson.synapse.org/Explore/Datasets/DetailsPage?datasetId=syn12976694
I'm fairly certain this is because these data were populated using get-geo-annotations.R, which has the following offending line:
Iterate over each of the GSMs associated with this GSE
metadata.tbl <- ldply(sampleNames(phenoData(gse.geo[[1]])),
Note that '[[1]]' above -- gse.geo is a list and I never understood why, so I naively just took the first element. I still don't know why, though I suspect it may be that each list element corresponds to a different platform. e.g., the example above was data generated on both the HiSeq 2500 and NextSeq 500.
This is a larger issue beyond this one dataset and I'm not going to attempt to fix it now.