Hi Elizabeth, Thanks for your reply. In fact, I tried plotDensity and the distribution looks bimodal for some arrays (this makes me worry a bit). I have 126 arrays and it is difficult to locate which array's distribution is deviated from others. I am trying to add legend to plotDensity and also like to add different colors to different conditions (something like what 'affycoretools' does). It will be easy for me to do such things if I am able to extract the raw intensity values. Are there ways to do that? Where can I find information about readUnits or extractMatrix?
Thanks again, Anbarasu On Apr 21, 6:37 pm, Elizabeth Purdom <epur...@gmail.com> wrote: > Hi Anbarasu, > You can do a few things. With plotDensity, you can plot the density of > the probes before and after. You can also do image plots of the before > and after. Or you can pull up the raw residuals for groups of genes > (rather than all of them at a time) using readUnits on the before and > after objects. > Best, > Elizabeth > > anbarasu wrote: > > Hi, > > > I am trying to check the quality of Human Exon 1.0 ST arrays before > > and after normalization. I am using the HuEx-1_0-st- > > v2,coreR3,A20071112,EP.cdf file. When I use: raw <- extractMatrix > > (csBC,verbose=verbose), I have got the following error messg: > > > 20090421 16:31:08|Getting data for the array set... > > 20090421 16:31:08| Allocating matrix... > > Error in matrix(naValue, nrow = ncells, ncol = nbrOfArrays) : > > cannot allocate vector of length 825753600 > > 20090421 16:31:08| Allocating matrix...done > > 20090421 16:31:08|Getting data for the array set...done > > > It seems that I don't have enough memory (I am using macpro with 4GB > > RAM). Is there any alternate ways to compare probe intensity values > > before and after normalization? BTW, where can I find the > > documentation of function: extractMatrix? > > > Thanks in advance. > > > Kind regards, > > Anbarasu --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
