How to export subset of metadata and expression data from BioConductor GEOquery?

Question

[William]

I am planning to use Bioconductor GEOquery to download a couple of micro-array datasets from NCBI GEO.

Then I would like to export a subset of the metadata and the expression data to flat files that I can import elsewhere.

What I have so far is:

library(GEOquery)
library("R.utils")

geo_id <- "GSE45016"
gse <- getGEO(geo_id,GSEMatrix=FALSE)

#show metadata
Meta(gse)

#show metadata for first sample
GSMList(gse)[[1]]

#select specific field from metadata of first sample
GSMList(gse)[[1]]@header$characteristics_ch1

# Result for sample 1
[1] "tissue: normal prostate (NP) epithelial cells"

GSMList(gse)[[2]]@header$characteristics_ch1

# Result for sample 2
[1] "tissue: prostate cancer cells"   "clinical stage: clinical T4N0M1"
[3] "gleason score: GS 9"             "psa level: PSA 5477ng/ml"

As you can see the number of key value pairs is different for sample 1 and 2. What is would like to have is an array for every key under

@header$characteristics_ch1

and then the value or null (in case the key is missing) for every sample in the GEO dataset" ;

key_tissue: normal prostate (NP) epithelial cells\tprostate cancer cells
key_psa_level: null\tPSA 5477ng/ml

Other metadata fields like "title" luckily only have a single value beneath it.

GSMList(gse)[[1]]@header$title = "Normal prostate"
GSMList(gse)[[2]]@header$title = "High-grade PC1"

Also these I would like to have in an array for the key title.

My second question is how to export the expressions data that is stored under every sample. I would like to stream trough all the probes, get the expression values for that probe for each sample and write it to another csv file.

Answer 1

[Neilfws]

I think that the way you have chosen to read the GSE data into R has created some confusion for you.

Try this instead (note: formatting was lost here so posted as a Gist):

As for exporting the expression data:

exp <- exprs(gse)

returns a matrix where the column names are sample names.

[Shicheng Guo]

Hi Neilfws, How did you write this reply? first it is in the gitbub and second how to prepare them in gitbub? thanks.

[Sean Davis]

Nicely done.