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 -~----------~----~----~----~------~----~------~--~---
