Parsing gene expression value for a list of genes from GEO

Question

I am looking for the gene expression data in GEO GSE15543 with the following keywords,

(Pancreatic Beta Cells) AND "Homo sapiens"[porgn:__txid9606]

I would like to parse the gene expression value of a list of genes from all the samples reported in any particular study.I understand there are two different formats for downloading datasets, SOFT and MINiML.

I have downloaded the soft.gz file and I am using BioConductor to read the contents from soft file using the instructions given here . The file has the content that I 'm looking for , I have checked the contents on the geo2r webpage. I'm still facing challenge in finding out how to fetch out the gene expression values for a list of genes. Any suggestions?

From the files that I download, I wish to parse the gene expression value and the Sample Title and Sample Description so that I can classify the values based on disease state and control state. Any suggestions on which format can be downloaded for the above-mentioned task?

Answer 1

GEO provides a GUI for this (just click on the "Analyze with GEO2 button"), you can even check/download the R/Bioconductor code used for the analyses.

Basically you will create groups of samples to compare/contrast and R/Bioconductor will run behind the scenes. Here is a nice tutorial.