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"
>
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>



      
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