<p>Here is what I am doing:</p>

<pre>
#GDS download and processing test
source(&quot;http://bioconductor.org/biocLite.R&quot;)
biocLite()
library(GEOquery)
gds &lt;- getGEO(&#39;GDS756&#39;)
#Convert to ExpressionSet
eset &lt;- GDS2eSet(gds,do.log2=TRUE)</pre>

<p>eset is summarized like this:</p>

<pre>
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 6 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM21712 GSM21713 ... GSM21718 (6 total)
  varLabels: sample disease.state description
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total)
  fvarLabels: ID Gene title ... GO:Component ID (21 total)
  fvarMetadata: Column labelDescription
experimentData: use &#39;experimentData(object)&#39;
  pubMedIds: 16531451 
Annotation: </pre>

<p>What I want is to output a table in a text file, containing the following columns: (Affymetrix probe ID, ENTREZ Gene ID, expression for sample 1, ..., expression for sample n).</p>

<p>Weirdly enough, GEOQuery manual says that eset should not contain annotated genes, but it seems from my basic object inspection that the featureData contains just that. However my R knowledge is limited so I was unable to produce my table from it.</p>

<pre>
write.table(data.frame(fData(eset),exprs(eset)),file=&quot;expression.txt&quot;,row.names=FALSE,sep=&quot;\t&quot;)</pre>
