[BioC] GCRMA: feature request

[bmb at bmbolstad.com]

At least in theory you should be able to accomplish this also via
affyPLM's threestep() function, though I have not tested against any
modifications that might have occured to GCRMA in the last 3-4 years.

eg

eset <-
threestep(abatch,background.method="GCRMA",normalize.method="quantile",summary.method="rlm")

also fitPLM() should accept the background.method="GCRMA" argument.





> Dear Jean,
>
> Please allow me to put forward a feature request for the GCRMA package:
> as you may have noticed in literature and on the BioC mailing list, there
> has been discussion on the use of the median polish algorithm (in RMA) for
> summerizing signals of probes into a single probeset value in relation to
> correlation artefacts. See e.g.:
> http://www.biomedcentral.com/1471-2105/11/553
> and
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/32255/focus=32259
>
> Moreover, in the above-mentioned BioC thread it is advocated to use a
> robust regression M-estimation procedure, e.g. available in the package
> 'affyPLM' / 'preprocessCore', instead of applying median polish on the
> transposed data matrix (aka tRMA), as was suggested by the authors of
> before-mentioned paper.
>
> In the intro of the fRMA paper it is also stated that more statistically
> rigorous procedures such as M-estimation techniques could be used for
> summerization, and this is one of the reasons fRMA by default uses
> AffyPLM's default M-estimator (Huber) for summerization instead of median
> polish.
> http://dx.doi.org/10.1093/biostatistics/kxp059
>
> Since AFAIK GCRMA is equal to RMA, except of course for the background
> correction, I wondered whether it would be possible to build in GCRMA the
> option to give a user the possibility to select a robust M-estimation
> procedure (e.g. affyPLM's default one) over the (GCRMA's default) median
> polish algorithm to summerize the probe data into a probeset values. Thus
> something like:
> x.norm <- gcrma(affy.data, sum="median.polish") [default] or x.norm <-
> gcrma(affy.data, sum="affyPLM").
>
> I would appreciate your opinion on this.
>
> Regards,
> Guido
>
>
> In addition, i would like to remind you about another issue with GCRMA my
> collegue Philip brought forward last December, which you may have missed
> (i copied his email below):
> -----------------------------------------------------------------------------
> I noticed the following problem when using gcRMA. the gcRMA-library tries
> to install probe packages. This is fine, except in cases when a
> probe-package is already available (and local versions vs repository
> versions do not necessarily match)! This behaviour is triggered within the
> function getProbePackage:
>
> function (probepackage, lib = .libPaths()[1], verbose = TRUE)
> {
>     options(show.error.messages = FALSE)
>     attempt <- try(do.call(library, list(probepackage, lib.loc = lib)))
>     options(show.error.messages = TRUE)
>
> ...
> }
>
> .libPaths() is in this particular example:
>> .libPaths()
> [1] "/local/home/guidoh/R/x86_64-unknown-linux-gnu-library/2.12"
> [2] "/geninf/prog64/R/R-2.12.0/lib64/R/library"
>
> As you can see, .libPaths()[1] point the the local R directory of the
> user, whereas the R installation directory is in .libPaths()[2]. Hence, we
> have the complication that gcRMA installs (the wrong) probe libraries
> (from BioC) that are already available to the user! The issue with this is
> that in some cases we use custom, tailored libraries that are not
> identical to those in the repositories. Hence, we may run into unexpected
> problems! As a matter of fact, I prefer to simply disable the ability (in
> gcRMA) to automatically install probe packages in the first place (just an
> option that is enabled by default, but can be disabled by the user)!
>
> Anyway, there is no reason to limit yourself to the first library. As an
> example, the following command will work without any problem:
>> attempt <- try(do.call(library, list("nugohs1a520180hsentrezgcdf",
>> lib.loc = .libPaths())))
>> attempt
>  [1] "gcrma"                      "nugohs1a520180hsentrezgcdf"
>  [3] "affy"                       "Biobase"
>  [5] "stats"                      "graphics"
>  [7] "grDevices"                  "utils"
>  [9] "datasets"                   "methods"
> [11] "base"
>
> At least your function will really go through all R library directories to
> search whether or not a library is installed!
> So I kindly ask for the following modifications:
> 1. An option in gcRMA to simply disable the automated installation of
> missing libraries [I need to control what happens! :)]
> 2. To simply use .libPaths() instead of .libPaths()[1] to really search
> through all R installation directories.
>
> Please let me know whether or not you agree. Doing these 2 modifications
> are not very hard, so I can contribute it to you if you are interested.
>
> Regards,
> Philip
>
>
> 	[[alternative HTML version deleted]]
>
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