GEOquery Meta
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David Lyon ▴ 340
@david-lyon-4016
Last seen 2.4 years ago
United States
Hi 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 Meta(gds535) [1] "able_begin" $channel_count [1] "1" $description [1] "Analysis of mechanisms of prostate cancer resistance to antiandrogen therapy. Isogenic hormone-sensitive and drug-resistant hormone-refractory xenograft pairs examined." $feature_count [1] "12651" $order [1] "none" $platform [1] "GPL91" $platform_organism [1] "Homo sapiens" $platform_technology_type [1] "in situ oligonucleotide" $pubmed_id [1] "14702632" $reference_series [1] "GSE847" $sample_count [1] "14" $sample_organism [1] "Homo sapiens" $sample_type [1] "RNA" $title [1] "Prostate cancer antiandrogen resistance" $type [1] "gene expression array-based" $update_date [1] "Mar 30 2004" $value_type [1] "count"
Cancer Prostate Cancer Prostate • 1.8k views
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@sean-davis-490
Last seen 12 weeks ago
United States
On Wed, Jun 9, 2010 at 1:45 PM, David Lyon <david_lyon3@yahoo.com> wrote: > Hi > > 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 > " > > Hi, David. library(GEOquery) gds535=getGEO("GDS535") Columns(gds535) Or, better: gds535ESet = GDS2eSet(gds535) Now, gds535ESet is an ExpressionSet and you can use the usual ExpressionSet methods to get the information you like. Sean > > Thanks again > > > > > The following is what Metadata that is capture from GDS535.soft using the > Meta function > Meta(gds535) > [1] "able_begin" > $channel_count > [1] "1" > $description > [1] "Analysis of mechanisms of prostate cancer resistance to antiandrogen > therapy. Isogenic hormone-sensitive and drug-resistant hormone- refractory > xenograft pairs examined." > $feature_count > [1] "12651" > $order > [1] "none" > $platform > [1] "GPL91" > $platform_organism > [1] "Homo sapiens" > $platform_technology_type > [1] "in situ oligonucleotide" > $pubmed_id > [1] "14702632" > $reference_series > [1] "GSE847" > $sample_count > [1] "14" > $sample_organism > [1] "Homo sapiens" > $sample_type > [1] "RNA" > $title > [1] "Prostate cancer antiandrogen resistance" > $type > [1] "gene expression array-based" > $update_date > [1] "Mar 30 2004" > $value_type > [1] "count" > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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HI Sean That works, Thank You very much. ________________________________ From: Sean Davis <sdavis2@mail.nih.gov> Cc: bioconductor@stat.math.ethz.ch Sent: Wed, June 9, 2010 2:36:18 PM Subject: Re: [BioC] GEOquery Meta >Hi > >>How do I get all the meta data from a gds GEO file? > >>For example Meta(gds535) gives all the metadata from DATASET as below but it doesnt return the metadata associated with the SUBSET eg > >>for GDS535.soft the Meta function "Meta(gds535)" doesnt return the following, is there a way to retrieve this information apart from going directly into it with perl > >>" >>^SUBSET = GDS535_1 >>!subset_dataset_id = GDS535 >>!subset_description = hormone-sensitive >>!subset_sample_id = GSM13066,GSM13068,GSM13070,GSM13073,GSM13075,GSM13077,GSM13079 >>!subset_type = cell type >>^SUBSET = GDS535_2 >>!subset_dataset_id = GDS535 >>!subset_description = hormone-refractory >>!subset_sample_id = GSM13065,GSM13067,GSM13069,GSM13072,GSM13074,GSM13076,GSM13078 >>!subset_type = cell type >>" > > Hi, David. library(GEOquery) gds535=getGEO("GDS535") Columns(gds535) Or, better: gds535ESet = GDS2eSet(gds535) Now, gds535ESet is an ExpressionSet and you can use the usual ExpressionSet methods to get the information you like. Sean >>Thanks again > > > > >>The following is what Metadata that is capture from GDS535.soft using the Meta function >>Meta(gds535) >>[1] "able_begin" >>$channel_count >>[1] "1" >>$description >>[1] "Analysis of mechanisms of prostate cancer resistance to antiandrogen therapy. Isogenic hormone-sensitive and drug-resistant hormone-refractory xenograft pairs examined." >>$feature_count >>[1] "12651" >>$order >>[1] "none" >>$platform >>[1] "GPL91" >>$platform_organism >>[1] "Homo sapiens" >>$platform_technology_type >>[1] "in situ oligonucleotide" >>$pubmed_id >>[1] "14702632" >>$reference_series >>[1] "GSE847" >>$sample_count >>[1] "14" >>$sample_organism >>[1] "Homo sapiens" >>$sample_type >>[1] "RNA" >>$title >>[1] "Prostate cancer antiandrogen resistance" >>$type >>[1] "gene expression array-based" >>$update_date >>[1] "Mar 30 2004" >>$value_type >>[1] "count" > >>_______________________________________________ >>Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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