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