Along with chapter 18 of Lewis, R for Medicine and Biology
- Installing the packages
source("http://bioconductor.org/biocLite.R") biocLite("simpleaffy") biocLite("GEOquery")
GEOquery
- Gene Expression Omnibus Repository (GEO)
- public repository
- allows submitting of high-throughput experimental data for free access by others
- includes single- and dual-channel microarrays, measuring mRNA, miRNA, genomic DNA (incl. arrayCGH and SNP) and protein abundance
- also contains a collection of web-based tools for querying and downloading of datasets
- for R there exists the GEOquery package
- public repository
- sample dataset: Polycystic ovary syndrome: adipose tissue
- get data
library(GEOquery) gds <- getGEO("GDS2084") Meta(gds)
Using locally cached version of GDS2084 found here: /tmp/Rtmpa2mlCM/GDS2084.soft.gz $channel_count [1] "1" $dataset_id [1] "GDS2084" "GDS2084" $description [1] "Analysis of omental adipose tissues of morbidly obese patients with polycystic ovary syndrome (PCOS). PCOS is a common hormonal disorder among women of reproductive age, and is characterized by hyperandrogenism and chronic anovulation. PCOS is associated with obesity." [2] "control" [3] "polycystic ovary syndrome" $email [1] "geo@ncbi.nlm.nih.gov" $feature_count [1] "22283" $institute [1] "NCBI NLM NIH" $name [1] "Gene Expression Omnibus (GEO)" $order [1] "none" $platform [1] "GPL96" $platform_organism [1] "Homo sapiens" $platform_technology_type [1] "in situ oligonucleotide" $pubmed_id [1] "17062763" $ref [1] "Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6" $reference_series [1] "GSE5090" $sample_count [1] "15" $sample_id [1] "GSM114841,GSM114844,GSM114845,GSM114849,GSM114851,GSM114854,GSM114855" [2] "GSM114834,GSM114842,GSM114843,GSM114847,GSM114848,GSM114850,GSM114852,GSM114853" $sample_organism [1] "Homo sapiens" $sample_type [1] "RNA" $title [1] "Polycystic ovary syndrome: adipose tissue" $type [1] "Expression profiling by array" "disease state" [3] "disease state" $update_date [1] "Mar 21 2007" $value_type [1] "count" $web_link [1] "http://www.ncbi.nlm.nih.gov/geo"
- display individual expression values
- first column (ID_REF): probe ID assigned by Affymetrix for each probe
- second column (IDENTIFIER): ID for the corresponding transcript
- remaining columns: expression values returned for each array
- first column (ID_REF): probe ID assigned by Affymetrix for each probe
Table(gds)[1:10,1:5]
ID_REF IDENTIFIER GSM114841 GSM114844 GSM114845 1 1007_s_at DDR1 222.6 252.7 219.3 2 1053_at RFC2 35.5 24.5 23.4 3 117_at HSPA6 41.5 53.3 31.3 4 121_at PAX8 229.8 419.6 274.5 5 1255_g_at GUCA1A 14.3 13 29.6 6 1294_at UBA7 150.8 116 89.9 7 1316_at THRA 29.7 35.4 53 8 1320_at PTPN21 35.1 44.8 28.8 9 1405_i_at CCL5 47.8 53.2 41.7 10 1431_at CYP2E1 22.5 24.9 38.7
- get disease status associated with each sample
Columns(gds)[,1:2]
sample disease.state 1 GSM114841 control 2 GSM114844 control 3 GSM114845 control 4 GSM114849 control 5 GSM114851 control 6 GSM114854 control 7 GSM114855 control 8 GSM114834 polycystic ovary syndrome 9 GSM114842 polycystic ovary syndrome 10 GSM114843 polycystic ovary syndrome 11 GSM114847 polycystic ovary syndrome 12 GSM114848 polycystic ovary syndrome 13 GSM114850 polycystic ovary syndrome 14 GSM114852 polycystic ovary syndrome 15 GSM114853 polycystic ovary syndrome
- information about source of samples
Columns(gds)[,3]
[1] "Value for GSM114841: EP3_adipose_control; src: Omental adipose tissue" [2] "Value for GSM114844: EP23_adipose_control; src: Omental adipose tissue" [3] "Value for GSM114845: EP31_adipose_control_rep1; src: Omental adipose tissue" [4] "Value for GSM114849: EP37_adipose_control; src: Omental adipose tissue" [5] "Value for GSM114851: EP49_adipose_control; src: Omental adipose tissue" [6] "Value for GSM114854: EP69_adipose_control; src: Omental adipose tissue" [7] "Value for GSM114855: EP71_adipose_control; src: Omental adipose tissue" [8] "Value for GSM114834: EP1_adipose_pcos_rep1; src: Omental adipose tissue" [9] "Value for GSM114842: EP10_adipose_pcos; src: Omental adipose tissue" [10] "Value for GSM114843: EP18_adipose_pcos; src: Omental adipose tissue" [11] "Value for GSM114847: EP32_adipose_pcos; src: Omental adipose tissue" [12] "Value for GSM114848: EP34_adipose_pcos; src: Omental adipose tissue" [13] "Value for GSM114850: EP47_adipose_pcos; src: Omental adipose tissue" [14] "Value for GSM114852: EP55_adipose_pcos; src: Omental adipose tissue" [15] "Value for GSM114853: EP66_adipose_pcos; src: Omental adipose tissue"
- get data
- get information in more detail for the first sample (GSM114841)
gsm <- getGEO("GSM114841") Meta(gsm)
Using locally cached version of GSM114841 found here: /tmp/Rtmpa2mlCM/GSM114841.soft $biomaterial_provider_ch1 [1] "Ramón y Cajal Hospital, Madrid, Spain" $channel_count [1] "1" $characteristics_ch1 [1] "Morbidly obese control subject" $contact_address [1] "ARTURO DUPERIER" $contact_city [1] "MADRID" $contact_country [1] "Spain" $contact_email [1] "bperal@iib.uam.es" $contact_fax [1] "34 91 5854401" $contact_institute [1] "INSTITUTO DE INVESTIGACIONES BIOMEDICAS, CSIC-UAM" $contact_name [1] "BELEN,,PERAL" $contact_phone [1] "34 91 5854478" $contact_state [1] "MADRID" $`contact_zip/postal_code` [1] "28029" $data_processing [1] "MAS 5.0, scaled to 100 and RMA" $data_row_count [1] "22283" $description [1] "Total RNA was extracted from omental adipose tissue from a control subject" $geo_accession [1] "GSM114841" $label_ch1 [1] "Biotin" $last_update_date [1] "Jun 16 2006" $molecule_ch1 [1] "total RNA" $organism_ch1 [1] "Homo sapiens" $platform_id [1] "GPL96" $series_id [1] "GSE5090" $source_name_ch1 [1] "Omental adipose tissue" $status [1] "Public on Jun 17 2006" $submission_date [1] "Jun 16 2006" $supplementary_file [1] "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM114nnn/GSM114841/suppl/GSM114841.CEL.gz" [2] "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM114nnn/GSM114841/suppl/GSM114841.EXP.gz" $taxid_ch1 [1] "9606" $title [1] "EP3_adipose_control" $type [1] "RNA"
- look at the additional data
Columns(gsm)
ID_REF VALUE Signal intensity - MAS 5.0, scaled to 100 and RMA ABS_CALL Presence/absence of gene transcript in sample; the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC) Detection p-value p-value that indicates the significance level of the detection call - so there are four columns
- probe ID
- expression value (output from a Mas 5.0 analysis software)
- Detection Call
- p-val (Detection p-val)
- probe ID
Table(gsm)[500:510,]
Column 1 ID_REF 2 VALUE 3 ABS_CALL 4 Detection p-value Description 1 2 Signal intensity - MAS 5.0, scaled to 100 and RMA 3 Presence/absence of gene transcript in sample; the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC) 4 p-value that indicates the significance level of the detection call ID_REF VALUE ABS_CALL Detection p-value 500 33307_at 47.8 P 0.039365 501 33304_at 35.3 A 0.339558 502 33197_at 58.4 P 0.017001 503 33148_at 21.4 P 0.019304 504 33132_at 15.8 A 0.189687 505 32837_at 274 P 0.000959 506 32836_at 319.8 P 0.006532 507 32811_at 213.3 P 0.024711 508 32723_at 35 P 0.004863 509 32699_s_at 43.9 A 0.162935 510 32625_at 67.1 A 0.11716 - look at the additional data
- get a series record
- contains lists for GPL platform object and the GSM sample record object
- retrieve GSE data structure for our example in one go
gse <- getGEO("GSE5090") gse
Found 1 file(s) GSE5090_series_matrix.txt.gz Using locally cached version: /tmp/Rtmpa2mlCM/GSE5090_series_matrix.txt.gz Using locally cached version of GPL96 found here: /tmp/Rtmpa2mlCM/GPL96.soft $GSE5090_series_matrix.txt.gz ExpressionSet (storageMode: lockedEnvironment) assayData: 22283 features, 17 samples element names: exprs protocolData: none phenoData sampleNames: GSM114834 GSM114840 ... GSM114855 (17 total) varLabels: title geo_accession ... data_row_count (30 total) varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total) fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total) fvarMetadata: Column Description labelDescription experimentData: use 'experimentData(object)' Annotation: GPL96
- contains lists for GPL platform object and the GSM sample record object
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