Entering edit mode
2.3 years ago
Lunky
▴
30
I used the following code to download and explore my data set, however I do not see the "Age" data for my samples in any of the clinical data columns, even when I examine the clinical data columns, such as "description":
gdat <- getGEO('GSE52401',
GSEMatrix=TRUE,
getGPL=FALSE)
gse <- gdat$GSE52401_series_matrix.txt.gz
mdat <- exprs(gse)
clindat <- pData(gse)
colnames(clindat)
# [1] "title" "geo_accession" "status" "submission_date"
# [5] "last_update_date" "type" "channel_count" "source_name_ch1"
# [9] "organism_ch1" "characteristics_ch1" "characteristics_ch1.1" "characteristics_ch1.2"
# [13] "molecule_ch1" "extract_protocol_ch1" "label_ch1" "label_protocol_ch1"
# [17] "taxid_ch1" "hyb_protocol" "scan_protocol" "description"
# [21] "description.1" "data_processing" "platform_id" "contact_name"
# [25] "contact_email" "contact_phone" "contact_institute" "contact_address"
# [29] "contact_city" "contact_state" "contact_zip/postal_code" "contact_country"
# [33] "supplementary_file" "data_row_count" "disease state:ch1" "gender:ch1"
# [37] "sample type:ch1"
Am I missing something? My apologies if this is obvious, it is my first time looking at GEO data.
If it's not in these columns you listed then it is not there. There is no rule what authors have to upload. If they used information in the paper that is not listed you can try emailing them.
Ah okay, thank you.