How to annotate probes to a GEO serie matrix?
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Entering edit mode
16 months ago

Hello!,

I am working with a GEO series matrix file (ID > GSE48452, Platform GPL11532) that corresponds to HuGene-1_1st Affymetrix Human Gene 1.1 ST array. I want to have the probes with the annotations, for example: Gene Symbol in order to create a data table like the following:

                 Sample1       Sample2  Sample3 Sample4 Sampl5  
    #CLASS:CANCER   case    case    case    case    
    #CLASS:SEX  F   F   M   M   F   M   F   M
 Gene Symbol  
  Gene1           -3.06 -2.25   -1.15   -6.64   0.4        
    Gene2          -1.36    -0.67   -0.17   -0.97   -2.0
    Gene3           1.61    -0.27    0.71        -0.62  0.14        
    Gene4           0.93    1.29           -0.23          -0.74          -2

How can map the probes with the gene symbol mantaining the order?

I was using the following Rscript without sucess, I don't know how to proceed........

getGEOdataObjects <- function(x, getGSEobject=FALSE){
  # Make sure the GEOquery package is installed
  require("GEOquery")
  # Use the getGEO() function to download the GEO data for the id stored in x
  GSEDATA <- getGEO(x, GSEMatrix=T, AnnotGPL=FALSE)
  # Inspect the object by printing a summary of the expression values for the first 2 columns
  print(summary(exprs(GSEDATA[[1]])[, 1:2]))

  # Get the eset object
  eset <- GSEDATA[[1]]
  # Save the objects generated for future use in the current working directory
  save(GSEDATA, eset, file=paste(x, ".RData", sep=""))

  # check whether we want to return the list object we downloaded on GEO or
  # just the eset object with the getGSEobject argument
  if(getGSEobject) return(GSEDATA) else return(eset)
}
# Store the dataset ids in a vector GEO_DATASETS just in case you want to loop through several GEO ids
GEO_DATASETS <- c("GSE48452")

# Use the function we created to return the eset object
eset <- getGEOdataObjects(GEO_DATASETS[1])
# Inspect the eset object to get the annotation GPL id
eset 
# Get the annotation GPL id (see Annotation: GPL10558)
gpl <- getGEO('GPL11532', destdir=".")
Meta(gpl)$title

# Inspect the table of the gpl annotation object
colnames(Table(gpl))

# Get the gene symbol and entrez ids to be used for annotations
Table(gpl)[1:10, c(1, 2, 6, 12)]
dim(Table(gpl))

# Get the gene expression data for all the probes with a gene symbol
geneProbes <- which(!is.na(Table(gpl)$Symbol))
probeids <- as.character(Table(gpl)$ID[geneProbes])

probes <- intersect(probeids, rownames(exprs(eset)))
length(probes)

geneMatrix <- exprs(eset)[probes, ]

inds <- which(Table(gpl)$ID %in% probes)
# Check you get the same probes
head(probes)
head(as.character(Table(gpl)$ID[inds]))

# Create the expression matrix with gene ids
geneMatTable <- cbind(geneMatrix, Table(gpl)[inds, c(1, 2, 6, 12)])
head(geneMatTable)

# Save a copy of the expression matrix as a csv file
write.csv(geneMatTable, paste(GEO_DATASETS[1], "_DataMatrix.csv", sep=""), row.names=T)

Thank you in advance for your help!!!!

R microarrays • 993 views
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Entering edit mode

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

Thank you!

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Entering edit mode
16 months ago
MatthewP ▴ 920

I recommend use left_join function from R package dplyr.

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