[BioC] GEOquery on rawdata and processed data ?

[Saroj Mohapatra]

There are links to the .CEL files (I guess this would be "raw" files) at 
GEO.

E.g., GSM72287 is part of the series GSE3218. At the bottom of the page 
(below) there is a link under 'Supplementary files'.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3218

HTH

Saroj


Alex Tsoi wrote:

>I figure out that those are the RMA-processed data, so my question should be
>how could I get the rawdata ?
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>On 7/3/07, Alex Tsoi <tsoi.teen at gmail.com> wrote:
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>>Dear all,
>>
>>I use the function getGEO from GEOquery to retrieve different cancer data
>>sets from GEO to do a meta-analysis.
>>
>>However, I am not quite sure if the data I downloaded has already been
>>processed (eg. RMA, or MAS) or not, is it true that all the
>>.CEL might be processed while all the .EXP files are raw ?
>>
>>Also, if I assign as:
>>
>>    
>>
>>>rawdata <- getGEO(GSM72287)
>>>      
>>>
>>"rawdata" has the data table with column names ID_REF and VALUE:
>>
>>but are those processed or raw data values ?
>>
>>My main goal is to get the raw data values from each sample so I could do
>>a meta analysis by applying my own processing
>>methods.
>>
>>Below is showing the rawdata.
>>
>>Greatly appreciate for any help.
>>
>>
>>
>>An object of class "GSM"
>>channel_count
>>[1] "1"
>>characteristics_ch1
>>[1] "mixed GCT (Embryonal Carcinoma, Seminoma)"
>>contact_address
>>[1] "1275 York Ave"
>>contact_city
>>[1] "New York"
>>contact_country
>>[1] "USA"
>>contact_department
>>[1] "Cell Biology"
>>contact_email
>>[1] " korkolaj at mskcc.org"
>>contact_institute
>>[1] "Memorial Sloan-Kettering"
>>contact_laboratory
>>[1] "Chaganti"
>>contact_name
>>[1] "James,,Korkola"
>>contact_phone
>>[1] "212-639-8281"
>>contact_state
>>[1] "NY"
>>contact_zip/postal_code
>>[1] "10021"
>>data_processing
>>[1] "RMA (robust multi-array)"
>>data_row_count
>>[1] "22645"
>>description
>>[1] "Adult Male Germ Cell Tumor"
>>extract_protocol_ch1
>>[1] "Frozen tissue from a germ cell tumor was minced and homogenized in
>>RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an
>>RNeasy kit (Qiagen)."
>>geo_accession
>>[1] "GSM72287"
>>hyb_protocol
>>[1] "standard Affymetrix procedures"
>>label_ch1
>>[1] "biotin"
>>label_protocol_ch1
>>[1] "Approximately 12 ug of total RNA was processed to produce
>>biotinylated cRNA targets."
>>last_update_date
>>[1] "Oct 12 2005"
>>molecule_ch1
>>[1] "total RNA"
>>organism_ch1
>>[1] "Homo sapiens"
>>platform_id
>>[1] "GPL97"
>>scan_protocol
>>[1] "standard Affymetrix procedures"
>>series_id
>>[1] "GSE3218"
>>source_name_ch1
>>[1] "germ cell tumor"
>>status
>>[1] "Public on Nov 10 2005"
>>submission_date
>>[1] "Aug 29 2005"
>>supplementary_file
>>[1] "file:///samples/GSM72287/GSM72287.CEL.gz"
>>[2] "file:///samples/GSM72287/GSM72287.EXP.gz"
>>title
>>[1] "germ cell tumors (GCT) and normal controls 052B 1"
>>type
>>[1] "RNA"
>>An object of class "GEODataTable"
>>****** Column Descriptions ******
>>  Column                     Description
>>1 ID_REF                              \t
>>2  VALUE RMA-calculated Signal intensity
>>****** Data Table ******
>>       ID_REF     VALUE
>>1 200000_s_at  9.913362
>>2   200001_at  9.822533
>>3   200002_at 11.318111
>>4 200003_s_at 12.280321
>>5   200004_at 11.068576
>>22640 more rows ...
>>
>>
>>
>>--
>>Lam C. Tsoi (Alex)
>>Medical University of South Carolina
>>    
>>
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