Hi Anbarasu. No, you don't have to remove all the files. What you can do is use extract() to extract the files that you are interested in, and create a new AffymetrixCelSet and fit the probe level modesl only on those samples. You do need to be careful though and I suggest you use *tags* so that the output results are sent to a different location on disk. Here is an example:
[...] # preprocessing as before csN1 <- extract(csN,1:12) # take a subset plmTr <- ExonRmaPlm(csN1, mergeGroups=TRUE, tag="*,subsetmerged") # add a tag fit(plmTr, verbose=verbose) # fit as normal Hope that helps. Mark On 04/08/2009, at 8:22 PM, anbarasu wrote: > > Dear All, > > I was able to run the human exon array analysis with 120 chips. I have > identified few outlier chips and would like to re-run the analysis > again without these outliers. Do I need to remove all files (in > plmData, probeData, and reports) that are created by aroma.affymetrix? > > Thanks in advance. > > Kind regards, > Anbarasu > > ------------------------------ 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 -~----------~----~----~----~------~----~------~--~---
