gravatar for Kevin Blighe

18 minutes ago by

Hello Silvia,

You can automatically obtain the phenotype data with the following code:

library(Biobase)
library(GEOquery)
gset <- getGEO("GSE75173", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL15034", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
pData(gset)

You are probably interested in 1 or more of the following columns:

cols <- c('title', 'geo_accession', 'source_name_ch1',
  'characteristics_ch1.1', 'characteristics_ch1.2',
  'characteristics_ch1.3', 'timepoint:ch1')

pData(gset)[,cols]
                                     title geo_accession
GSM1944594           Patient 001, baseline    GSM1944594
GSM1944595 Patient 001, 16 weeks tadalafil    GSM1944595
GSM1944596           Patient 002, baseline    GSM1944596
GSM1944597 Patient 002, 16 weeks tadalafil    GSM1944597
GSM1944598           Patient 003, baseline    GSM1944598
                              source_name_ch1
GSM1944594           PAH-SSc patient_baseline
GSM1944595 PAH-SSc patient_16 weeks tadalafil
GSM1944596           PAH-SSc patient_baseline
GSM1944597 PAH-SSc patient_16 weeks tadalafil
GSM1944598           PAH-SSc patient_baseline
                                                                  characteristics_ch1.1
GSM1944594 patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
GSM1944595 patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
GSM1944596 patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
GSM1944597 patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
GSM1944598 patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
                                      characteristics_ch1.2
GSM1944594                     timepoint: 0 weeks; baseline
GSM1944595 timepoint: after 16 weeks of tadalafil treatment
GSM1944596                     timepoint: 0 weeks; baseline
GSM1944597 timepoint: after 16 weeks of tadalafil treatment
GSM1944598                     timepoint: 0 weeks; baseline
                 characteristics_ch1.3                         timepoint:ch1
GSM1944594 clinical outcome: unchanged                     0 weeks; baseline
GSM1944595 clinical outcome: unchanged after 16 weeks of tadalafil treatment
GSM1944596  clinical outcome: negative                     0 weeks; baseline
GSM1944597  clinical outcome: negative after 16 weeks of tadalafil treatment
GSM1944598  clinical outcome: positive                     0 weeks; baseline

I trust that you can do the remaining part of connecting this to your WGCNA data.

Kevin

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modified 18 minutes ago

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18 minutes ago
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Kevin Blighe58k



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