Hi Cathy. Comments below.
On 29-Sep-09, at 10:11 PM, CathyMitchell wrote: > Hi all, > > I am using the gene st array and would like to know a couple of things > about the probe level model. After doing the RmaPlm one can do two > types of QC, the NUSE and RLE plots. These however compare results for > each array. I would like to be able to have a look at the individual > genes/probes (be able to flag up problem genes/probes). Is there a way > to plot these? For plotting individual genes, you may be interested in this page (and discussion): http://groups.google.com/group/aroma-affymetrix/web/using-the-genomegraphs-package-with-firma As another approach, you could simply plot the data as line plots (1 line for each sample, 1 point for every probe). For example, you could use extractMatrix() to read your normalization data into a matrix and then use matplot(). > Also is there an error reading for the probe level models? like a > splice index or something? I'm not sure exactly what you are after here. Are you looking for standard errors of the probe/chip effects? That information is not stored, although it is calculated from the underlying 'preprocessCore' package. If you are looking at doing something along the lines of differential splicing with Gene 1.0ST arrays, you might be interested in this (apologies for the shameless self-promotion): http://www.biomedcentral.com/1471-2105/10/156 Cheers, Mark > > Thanks, > Cathy > > ------------------------------ 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 -~----------~----~----~----~------~----~------~--~---
