We are trying to match the 691 EU_Code IDs included in the file ?ANMerge_gene_expression_normalized_under_90.csv? (syn22286804, https://www.synapse.org/#!Synapse:syn22286804) with the gexp_ids for accessing the Raw data available in GEO:
Batch 1: GSE63060 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63060)
Batch 2: GSE63061 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63061),
as suggested at https://www.synapse.org/#!Synapse:syn2795018 for the AddNeuroMed Data.
However, using the file ?id_mapping_file_updated.csv? (syn22023005, https://www.synapse.org/#!Synapse:syn22023005), we found that 24 EU_Code IDs do not correspond to any gexp_ids of the GEO raw data. Indeed, we could find a mapping only for 322 samples from Batch 1 and 345 samples from Batch 2. Where data for those 24 ANMerge samples come from?
The examination of the two files ?Chip_Subject_identifier_RIN_BATCH_1.csv? (syn5509449, https://www.synapse.org/#!Synapse:syn5509449) and ?Chip_Subject_identifier_RIN_BATCH_2.csv? (syn5509466, https://www.synapse.org/#!Synapse:syn5509466) revealed that the EU_CODE IDs for 18 samples appear in both files, but associated to different ?Chip_IDs?; so, probably, their mapping in file syn22023005 could have been deleted to avoid overlapping EU_Code IDs from the two batches. But still there are 6 missing associations.
Could you help solving this issue?
Thank you