Hi. On Fri, Sep 30, 2011 at 2:32 AM, rene.rotterdam <rene.boettche...@googlemail.com> wrote: > Hello Henrik, > > thank you very much for your help, I think I got the hang of it. What > I now would like to know: > > is there a way to perform the FIRMA analysis on an ExpressionSet > object? I want to combine several analysis methods without having to > rerun RMA for every single one of them, as they all have their own > object class.
Sorry, at least not via the Aroma framework. /Henrik > > Thank you very much in advance, > > Rene > > On Sep 21, 9:14 pm, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Hi, >> >> I'm not a expert on exon analysis, but I'll try to answer some of your >> questions. >> >> On Tue, Sep 13, 2011 at 5:45 AM, rene.rotterdam >> >> <rene.boettche...@googlemail.com> wrote: >> > Dear all, >> >> > I fairly new to the field of Exon Arrays and my experiences with >> > Microarrays in general are quite limited, so I have a couple of >> > questions concerning the analysis of Exon Array data. >> >> > First of all, I would like to do an RMA (or GCRMA) based on the >> > validated genes of the core probeset (so bg, qn + sum). The way I >> > understood the literature, this normalizes ALL probesets based on the >> > intensity values of the core probeset (which is also what I intend to >> > do). >> >> Actually, this depends on what settings/intermediate preprocessing >> methods you use. For instance, in vignette 'Human exon array >> analysis' [http://aroma-project.org/node/37] the quantile >> normalization step is: >> >> qn <- QuantileNormalization(csBC, typesToUpdate="pm") >> >> which says that it operates only on PM probes. The definition of what >> a PM probe is is defined by the CDF used. See also page 'Empirical >> probe-signal densities and rank-based quantile normalization' >> [http://aroma-project.org/node/141] for more information on how the >> settings for QuantileNormalization affect the outcome. >> >> > Afterwards, I want to extend my analysis on the full probeset, as >> > I will focus on some genes that are not included in 'core'. >> > I read about this procedure in a paper on APT and R by H. Lockstone >> > and wanted to implement it via aroma. >> >> The way the 'Human exon array analysis' vignette is outlined, changing >> to another CDF will affect what probes are considered PMs and hence >> also affect the preprocessing output. To me (my personal opinion) >> this is a bit unfortunate; ideally the early on preprocessing steps >> that are designed to normalize probe-level data (not summarized) >> should be invariant to the (CDF) annotation. An alternative approach >> is to use the "default" CDF throughout these steps, as done/suggested >> in thread 'Help Regarding GCRMA Human Exon' (Dec 2, 2010) >> [https://groups.google.com/forum/#!topic/aroma-affymetrix/QD6o-3XiifM/...]. >> >> >> >> > Am I mislead in this case? >> > I tried to realize this by doing a GCRMA on 'core', but the resulting >> > probe intensities are to few (~285k) and the probes I'm looking for >> > are not included. >> >> > Before that, I did a regular RMA on the full probeset and I got all >> > the probes /the intensities I was looking for, but I realized that >> > normalizing to not validated genes may not be the best idea. >> >> As I indicated above, from my experience with other chiptypes I >> *think* it is ok to probe-level normalization using the full CDF. >> However, I haven't investigated the impact of doing this, so I might >> be wrong. I leave it to others with more exon-array experience to >> comment on this/correct me. >> >> >> >> > It would be a great help if you could set my thoughts straight and if >> > I'm correct tell me how to use aroma to achieve what I want. >> >> > Note: I assembled my script as described in >> >http://aroma-project.org/node/37 >> > and >> >https://groups.google.com/forum/#!topic/aroma-affymetrix/QD6o-3XiifM/... >> >> FYI, it is always easier if you cut'n'paste you complete script to >> your message - avoids second guessing. >> >> Not much help, but at least some pointers and suggestions. >> >> /Henrik >> >> >> >> >> >> >> >> >> >> > Thank you in advance for your help. >> >> > With best regards, >> > Rene >> >> > -- >> > 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 with websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ > > -- > 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 with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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. 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