[BioC] (GC)RMA estimates without summerization?
James W. MacDonald
jmacdon at med.umich.edu
Mon Feb 11 21:47:37 CET 2008
I think you are looking at this from the wrong angle. Instead of doing
everything but the summarization step using a wrapper function, why
don't you just do the steps you want?
Hooiveld, Guido wrote:
> Dear list,
> I would like to obtain the GCRMA and RMA expression estimates per
> individual probe (thus not per probe set). In other words, I would like
> to apply the [default] (GC)RMA background correction and normalization,
> but not the summerization step (median polish). How to do this??
> I searched of course the mail archive but found no answer on this.
> I tried the 'expresso' and 'threestep' functions of AffyPLM, but for
> summerization it is not explicity stated that "summerization" argument
> can be "FALSE" or "NO" (or something else).
> When I nevertheless try to execute threestep I get the following error:
>> esetrma <- threestep(rawdata, background.method = "RMA.2",
> normalize.method="quantile", summary.method=FALSE)
> Error in get.summary.code(summary.method) :
> FALSE is not a valid summary method. Please use one of: median.polish
> tukey.biweight average.log rlm log.average log.median
> ...clearly indicating that threestep the "summary method" can not be
> omitted (as is also stated in the vignette).
> When I try to do this:
>> esetrma <- expresso(rawdata, bgcorrect.method = "rma",
> normalize.method="quantiles", pmcorrect.method="pmonly",
> background correction: rma
> normalization: quantiles
> PM/MM correction : pmonly
> expression values: FALSE
> background correcting...done.
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "computeExprSet", for
> signature "AffyBatch", "character", "logical"
> ... I got an error likely NOT related to the summary.method option, but
> to something else?? But I expect then even when solving this problem
> 'expresso' won't allow skipping the summerization step.
> Thus, how to omit "median polish" in RMA and GCRMA?
> R version 2.6.0 (2007-10-03)
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> attached base packages:
>  splines tools stats graphics grDevices utils datasets
> methods base
> other attached packages:
>  medicagocdf_2.0.0 affyPLM_1.14.0 gcrma_2.10.0
> matchprobes_1.10.0 affy_1.16.0
>  preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.0
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet: http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email: guido.hooiveld at wur.nl
> [[alternative HTML version deleted]]
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
More information about the Bioconductor