Hi, I have 10 microarray data sets (each data set related to a disease) in which I already compiled to get differentially expressed genes (DEGs) in every individual data set. I want to extract common DEGs of all the datasets, is there any tool/R package/R function to do it.

I have the ProbesetIDs, Genenames, GeneSymbols, Entrez IDs, LogFC values, B values, P values; in all the datasets.

Any help would be appreciated. Thanks!
<p>If I understand it correctly, you simply want to find the unique gene identifiers (or probe ids) that are differentially expressed in all experiments? One simple way to do that in R would be (here for three sets):</p>

<p><code>a = c(&#39;gene1&#39;,&#39;gene3&#39;,&#39;gene5&#39;,&#39;gene7&#39;,&#39;gene9&#39;)<br />
b = c(&#39;gene3&#39;,&#39;gene6&#39;,&#39;gene8&#39;,&#39;gene9&#39;,&#39;gene10&#39;)<br />
c = c(&#39;gene2&#39;,&#39;gene3&#39;,&#39;gene4&#39;,&#39;gene5&#39;,&#39;gene7&#39;,&#39;gene9&#39;)</code></p>

<p><code>Reduce(intersect, list(a,b,c))</code></p>

<p>[1] &quot;gene3&quot; &quot;gene9&quot;</p>

<p>On a side note, if you are requiring a gene to be <strong>significantly</strong> differentially expressed in all experiments, that is a fairly tough threshold. Since experiments typically do not have the power to detect all genes that are truly differentially expressed, you are likely to miss some in each set due to randomness. You could, alternatively, require that a gene is significantly differentially expressed in some samples, and has a fold change in the same direction (or over some meaningful threshold) in others.</p>
