I figure out that those are the RMA-processed data, so my question should be
how could I get the rawdata ?


On 7/3/07, Alex Tsoi <tsoi.teen@gmail.com> wrote:
>
> 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@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




-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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