reading gse series matrix data

Question

[cs18s003]

i wanted to read gse series matrix format data usign python but i just found one library called gse which seems to be an obsolete library. does anyone have experience of reading gse series matrix data using python .kindly point me to a useful resource

[Nitin Narwade]

I think you should look at GEOparse, it may help you.

I do not have any experience working with GEOparse, but I have used GEOquery (an R package, which is base for GEOparse) which will read GSE Series Matrix.

[cs18s003]

I am new to R ,i have been trying to write the gse series matrix data into a csv file and i am not getting the output in the proper way as i need . the result.txt below is generating me the output line by line i.e the attribute names on the first line and the corresponding value of the attributes for every samples in the next consecutive lines .i want them in a csv file. can u point me in the right direction . thanks in advance .

This is the code snippet i wrote below :

source("http://bioconductor.org/biocLite.R")

biocLite("GEOquery")

library("GEOquery")

gse=getGEO(filename="~/Downloads/GSE79362seriesmatrix.txt.gz",GSEMatrix=TRUE,getGPL = FALSE)

write.table(gse, file='results.txt')

[Nitin Narwade]

There is no expression data in the series matrix of GSE79362.

For this example, I have used GSE2553 GEO id and code will be something like this.

gse <- getGEO(filename="GSE2553_series_matrix.txt.gz",GSEMatrix = TRUE,getGPL = FALSE) #Retrieve matrix data and store it in R object
show(object = gse) ## To summarize the gse object
x <- exprs(object = gse) #Get expression set from gse object

write.csv(x = x, file = "GSE2553.expression.matrix.csv", quote = F, row.names = F) #export expression matrix in file (.csv format).