Hi, Mark: The other question i have is that even if I use the existing CDF file, some of the gene expression or probe level expressions are really low, like 1.1. It seemed to me t hat they are just too low. These were obtained after the background normalization etc. Is there any way that I can tell whether they are just background noise? I used Rmabackgroundcorrection
Thanks Sabrina On Sep 2, 6:17 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote: > Hi Sabrina. > > Hmm, that does seem unexpected. I would expect that if there are just > a few probes picked out, it shouldn't change that much. > > Can you give more details about this new CDF you made? Would it be > similar to the existing 'core' CDF? Presumably, there will be a large > overlap with the existing CDF. Can you verify this? And, give some > numbers on this. A few things like: total number of probes for each > CDF, for a given unit does it have a large overlap of probes, etc. > > The one thing that comes to mind is that maybe you've included a bunch > of the 'full' or 'extended' probes in your new CDF and this would > likely lower the average. > > Cheers, > Mark > > On 3-Sep-09, at 5:07 AM, sabrina shao wrote: > > > > > > > Hi, all > > I am working on mouse Exon arrays from Affy. Because there are probes > > with multiple hits on the genome, I screened out these probes and > > exons with only one probe and transcript clusters with one exon on the > > array. After that I created a CDF file as illustrated from this group. > > My problems is: when I checked the probe level expressions (not gene > > expression) , the average is about 4.5 , and the gene expression level > > ( not surprisingly) is about similar level. And the smallest probe > > level was about 1.1. I also used the CDF file I downloaded from aroma > > here, using the same program, I got the gene expression level around > > 6.2. That is about 1.7 fold change. and the results from the new CDF > > that I created was just too low. I can't figure it out why. Can anyone > > give me some suggestions and hints? Thanks > > > Sabrina > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robin...@garvan.org.au > e: mrobin...@wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
