<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>If you get the probe sequences, you should be able to map it back to the genome (a useful exercise anyway - sometimes the genome sequence has changed and the probes e.g. no longer map uniquely), and then you can use the latest gene annotations to figure out which specific exon they hit. From there, if you sort by transcript ID, you should be able to get an idea. There also seem to be some alternative splicing databases in existence, but I've never used them, so can't tell you anything about them: <a href='http://www.eurasnet.info/tools/asdatabases'>http://www.eurasnet.info/tools/asdatabases</a></p>
