Hi Mark, Thanks for the reply. I completely agree with you on the issue U133 arrays are 3' biased and thus the majority of the probes will be concentrated at the 3' end. However that being said, I've observed cases where the probes can be interrogating the 5' end and also near the middle of the gene. And this because even more prevalent when using a custom CDF like the ones which group probes based on the exonic region they are interrogating (http:// brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/ ense.asp).
But from a purely statistical view, there is no restriction on using FIRMA on u133 arrays right? Is there actually a way to run FIRMA on U133 arrays from aroma.affymetrix? Fong On Jan 14, 12:47 am, Mark Robinson <mrobin...@wehi.edu.au> wrote: > Hi Fong. > > Sorry for the delay in replying. > > I don't think FIRMA will work for U133 arrays, because of where the probes > interrogate. The U133 arrays have probes in the 3' region of the gene, > whereas the Gene/Exon arrays have probes along the whole transcript. That > said, there are often multiple probesets per gene on the U133 array, with the > intention being that these would interrogate different isoforms. > > Hope that helps. > > Mark > > On 2011-01-05, at 6:49 PM, Fong wrote: > > > > > Hi, > > > Is there any reason why the FIRMA method wouldn't work on HG-U133 Plus > > 2.0 Arrays? I fully understand that the method was originally > > designed to detect for alternative splicing in Human Exon arrays, but > > the same principles can be applied to the U133 Plus 2.0 Arrays can it > > not? Each FIRMA score is specific to a probeset per sample and the > > greater the magnitude the stronger the evidence of alternative > > splicing in that region for that particular sample. > > > In fact, it might provide a better estimate since there are typically > > 11 probes per probeset instead of the the usual 4 probes per probeset > > in Human Exon arrays. This should theoretically increase the > > sensitivity and robust of the FIRMA score calculation. > > > Fong > > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > > version of the package, 2) to report the output of sessionInfo() and > > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: mrobin...@wehi.edu.au > e: m.robin...@garvan.org.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > ______________________________________________________________________ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
