<p>GEO provides a GUI for this (just click on the &quot;Analyze with GEO2 button&quot;), you can even check/download the R/Bioconductor code used for the analyses.</p>
<p>Basically you will create groups of samples to compare/contrast and R/Bioconductor will run behind the scenes. Here is a nice <a href="https://www.youtube.com/watch?v=EUPmGWS8ik0" rel="nofollow noreferrer">tutorial</a>.</p>

CC BY-SA 4.0
2021-05-07T18:58:03.647Z
2021-05-07T18:58:03.647Z
haci
<p>I am looking for the gene expression data in <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15543" rel="nofollow noreferrer">GEO GSE15543</a> with the following keywords,</p>
<pre><code>(Pancreatic Beta Cells) AND &quot;Homo sapiens&quot;[porgn:__txid9606]
</code></pre>
<p>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.</p>
<p>I have downloaded the soft.gz file and I am using BioConductor to read the contents from soft file using the instructions given <a href="https://mdozmorov.github.io/BIOS567/assets/presentation_Bioconductor/GEO.pdf" rel="nofollow noreferrer">here</a> . 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?</p>
<p>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?</p>

<gene-expression><geoquery>
Parsing gene expression value for a list of genes from GEO
# Parsing gene expression value for a list of genes from GEO

(Asked by: username_0 on 2018-08-10)

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?

**Tags:** gene-expression, geoquery

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## 1 answers

### Answer by username_1 on 2021-05-07. Score: 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](https://www.youtube.com/watch?v=EUPmGWS8ik0).


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