Data extraction from GEO onto R

Question

[silsie645]

I am trying to extract my information from interest from the dataset GSE33113 from GEO onto R but R doesnot seem to recognize my data input. I tried:

gset<-getGEO('GSE33113',GSEMatrix=TRUE,getGPL=FALSE)
library(survival)
library(GEOquery)
library(RegParallel)
library(Biobase)
library(survminer)

#loading platform data 
gset<-getGEO('GSE33113',GSEMatrix=TRUE,getGPL=FALSE)

x<-exprs(gset[[1]])

#remove Affymetrix control probes 
x<-x[-grep('^AFFX', rownames(x)),]

#transform the expression data to Z scores
x<-t(scale(t(x)))

#extracting information of interest
idx<-which(colnames(pData(gset[[1]]))%in%c('Age_At_Diagnosis:ch1','Sex:ch1','Disease status:ch1','Tissue.ch1'))
metadata<-data.frame(pData(gset[[1]])[,idx],row.names=rownames(pData(gset[[1]])))

but the metadata generated only contained the 'sex' data even though I got this response:

#extract information of interest from the phenotype data 
> idx<-which(colnames(pData(gset[[1]]))%in%c('AgeAtDiagnosis:ch1','Death:ch1','Gender:ch1','Grading:ch1','LymphNodesInvaded:ch1','OverallSurvival_months:ch1','TumorFreeSurvival_months:ch1'))
> metadata1<-data.frame(pData(gset[[1]])[,idx],row.names=rownames(pData(gset[[1]])))

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[silsie645]

Ok thanks. I just saw your reply.

[silsie645]

Sorry the idx response was:

#extracting information of interest
> idx<-which(colnames(pData(gset[[1]]))%in%c('Age_At_Diagnosis:ch1','Sex:ch1','Disease status:ch1','Tissue.ch1'))
> metadata<-data.frame(pData(gset[[1]])[,idx],row.names=rownames(pData(gset[[1]])))

With 'Age_At_Diagnosis' column, I also tried 'Age at diagnosis' as seen in the dataset and 'AgeAtDiagnosis' but I got the same response.

Answer 1

[dsull]

Run the following:

print(colnames(pData(gset[[1]])))

You'll find that correct names of all the columns, e.g. the correct column name is age at diagnosis:ch1 not Age_At_Diagnosis:ch1