[BioC] GEOquery Meta

David Lyon david_lyon3 at yahoo.com
Wed Jun 9 19:45:02 CEST 2010


How do I get all the meta data from a gds GEO file?

For example Meta(gds535) gives all the metadata from DATASET as below but it doesnt return the metadata associated with the SUBSET eg

for GDS535.soft the Meta function "Meta(gds535)" doesnt return the following, is there a way to retrieve this information apart from going directly into it with perl

^SUBSET = GDS535_1
!subset_dataset_id = GDS535
!subset_description = hormone-sensitive
!subset_sample_id = GSM13066,GSM13068,GSM13070,GSM13073,GSM13075,GSM13077,GSM13079
!subset_type = cell type
^SUBSET = GDS535_2
!subset_dataset_id = GDS535
!subset_description = hormone-refractory
!subset_sample_id = GSM13065,GSM13067,GSM13069,GSM13072,GSM13074,GSM13076,GSM13078
!subset_type = cell type

Thanks again

The following is what Metadata that is capture from GDS535.soft using the Meta function
[1] "able_begin"
[1] "1"
[1] "Analysis of mechanisms of prostate cancer resistance to antiandrogen therapy. Isogenic hormone-sensitive and drug-resistant hormone-refractory xenograft pairs examined."
[1] "12651"
[1] "none"
[1] "GPL91"
[1] "Homo sapiens"
[1] "in situ oligonucleotide"
[1] "14702632"
[1] "GSE847"
[1] "14"
[1] "Homo sapiens"
[1] "RNA"
[1] "Prostate cancer antiandrogen resistance"
[1] "gene expression array-based"
[1] "Mar 30 2004"
[1] "count"

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