<p>Hi all,</p>

<p>I am working on microarray expression. I am new to this, so pardon me if I provide incomplete details.</p>

<p>I have downloaded the raw data from GEO (gilent-014850 Whole Human Genome Microarray 4x44K G4112F) and we want to look at expression levels of genes with different datasets added on top (expression levels of genes with and without epigenetic marks, transcription factors).</p>

<p>When I was extracting the information, I realised that there are multiple probes for certain genes. At first, I took the highest expression values for each gene and then later compared it with the average and the difference was notable. </p>

<p>I was wondering if there is a method to identify which probes are present in all isoforms and which are present in a few.</p>

<p>Thanks for the help.</p>

<p>Yes, I agree with mapping the probe sequences on your own.  However, I typically wouldn't do this prior to analysis - in practice, there are a lot of probes to check.</p>

<p>I would typically conduct differential expression with all the probes, and allow a single probe to be sufficient for differenital expression (at which point, I could take some time to understand any significant differences between multiple probes that map to the same gene - for specific results that look interesting).</p>

<p>Your strategy should depend upon your method of integration.  If you are looking for overlapping gene lists, I would recommend the strategy listed above.  However, if you need to work with the absolute expression values in the integration process and you need a single expression value per gene, I would typically just average the expression among probes that map to the same gene.</p>
