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BioStars 111791
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| gse <- getGEO("GSE45016") # you want GSEMatrix = TRUE | |
| # ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/ | |
| # Found 1 file(s) | |
| # GSE45016_series_matrix.txt.gz | |
| # trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/GSE45016_series_matrix.txt.gz' | |
| # ftp data connection made, file length 1486394 bytes | |
| # opened URL | |
| # ================================================== | |
| # downloaded 1.4 Mb | |
| # | |
| # File stored at: | |
| # /var/folders/7j/7r8lt_3s14s12jx4r2x_qc5c0000gn/T//Rtmpq73dcI/GPL570.soft | |
| # gse is a list of length 1 named after series matrix; let's tidy it up | |
| gse <- gse$GSE45016_series_matrix.txt.gz | |
| gse | |
| # ExpressionSet (storageMode: lockedEnvironment) | |
| # assayData: 54675 features, 11 samples | |
| # element names: exprs | |
| # protocolData: none | |
| # phenoData | |
| # sampleNames: GSM1095876 GSM1095877 ... GSM1095886 (11 total) | |
| # varLabels: title geo_accession ... data_row_count (34 total) | |
| # varMetadata: labelDescription | |
| # featureData | |
| # featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total) | |
| # fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total) | |
| # fvarMetadata: Column Description labelDescription | |
| # experimentData: use 'experimentData(object)' | |
| # Annotation: GPL570 | |
| # now get the phenotypic data (covariates etc.) using pData() | |
| pd <- pData(gse) | |
| names(pd) | |
| # [1] "title" "geo_accession" "status" "submission_date" "last_update_date" # | |
| # [6] "type" "channel_count" "source_name_ch1" "organism_ch1" "characteristics_ch1" | |
| # [11] "characteristics_ch1.1" "characteristics_ch1.2" "characteristics_ch1.3" "molecule_ch1" "extract_protocol_ch1" | |
| # [16] "label_ch1" "label_protocol_ch1" "taxid_ch1" "hyb_protocol" "scan_protocol" | |
| # [21] "description" "data_processing" "platform_id" "contact_name" "contact_email" | |
| # [26] "contact_department" "contact_institute" "contact_address" "contact_city" "contact_state" | |
| # [31] "contact_zip/postal_code" "contact_country" "supplementary_file" "data_row_count" | |
| # sample 1 is normal tissue so does not have cancer-specific data values | |
| pd$title | |
| # V2 V3 V4 V5 V6 V7 V8 V9 | |
| # Normal prostate High-grade PC1 High-grade PC2 High-grade PC3 High-grade PC4 High-grade PC5 High-grade PC6 High-grade PC7 | |
| # V10 V11 V12 | |
| # High-grade PC8 High-grade PC9 High-grade PC10 | |
| # 11 Levels: High-grade PC1 High-grade PC10 High-grade PC2 High-grade PC3 High-grade PC4 High-grade PC5 High-grade PC6 ... Normal prostate | |
| pd$characteristics_ch1 | |
| # V2 V3 V4 | |
| # tissue: normal prostate (NP) epithelial cells tissue: prostate cancer cells tissue: prostate cancer cells | |
| # V5 V6 V7 | |
| # tissue: prostate cancer cells tissue: prostate cancer cells tissue: prostate cancer cells | |
| # V8 V9 V10 | |
| # tissue: prostate cancer cells tissue: prostate cancer cells tissue: prostate cancer cells | |
| # V11 V12 | |
| tissue: prostate cancer cells tissue: prostate cancer cells | |
| # Levels: tissue: normal prostate (NP) epithelial cells tissue: prostate cancer cells | |
| pd$characteristics_ch1.1 | |
| # V2 V3 V4 V5 | |
| # clinical stage: clinical T4N0M1 clinical stage: clinical T4N1M1 clinical stage: clinical T2bN1M1 | |
| # V6 V7 V8 V9 | |
| # clinical stage: clinical T3aN0M1 clinical stage: clinical T3bN0M1 clinical stage: clinical T4N1M1 clinical stage: clinical T3bN1M1 | |
| # V10 V11 V12 | |
| # clinical stage: clinical T3bN0M0 clinical stage: clinical T3aN0M0 clinical stage: clinical T3aN1M0 | |
| # 10 Levels: clinical stage: clinical T2bN1M1 clinical stage: clinical T3aN0M0 ... clinical stage: clinical T4N1M1 | |
| pd$characteristics_ch1.2 | |
| # V2 V3 V4 V5 V6 V7 V8 | |
| # gleason score: GS 9 gleason score: GS 9 gleason score: GS 9 gleason score: GS 9 gleason score: GS 9 gleason score: GS 9 | |
| # V9 V10 V11 V12 | |
| # gleason score: GS 8 gleason score: GS 9 gleason score: GS 9 gleason score: GS 8 | |
| # Levels: gleason score: GS 8 gleason score: GS 9 | |
| pd$characteristics_ch1.3 | |
| # V2 V3 V4 V5 V6 | |
| # psa level: PSA 5477ng/ml psa level: PSA 4427ng/ml psa level: PSA1900ng/ml psa level: PSA 630ng/ml | |
| # V7 V8 V9 V10 V11 | |
| # psa level: PSA 334ng/ml psa level: PSA 311ng/ml psa level: PSA 1000ng/ml psa level: PSA 275ng/ml psa level: PSA 80ng/ml | |
| # V12 | |
| # psa level: PSA 234ng/ml | |
| # 11 Levels: psa level: PSA 1000ng/ml psa level: PSA 234ng/ml psa level: PSA 275ng/ml psa level: PSA 311ng/ml ... psa level: PSA1900ng/ml |
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