[BioC] (GC)RMA estimates without summerization?

[James W. MacDonald]

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?

?bg.correct
?normalize
?bg.adjust.gcrma

Best,

Jim



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",
> summary.method=FALSE)
> background correction: rma 
> normalization: quantiles 
> PM/MM correction : pmonly 
> expression values: FALSE 
> background correcting...done.
> normalizing...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?
>  
>  
> TIA,
> Guido
>  
>  
>  
>> sessionInfo()
> R version 2.6.0 (2007-10-03) 
> i386-pc-mingw32 
>  
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>  
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> methods   base     
>  
> other attached packages:
> [1] medicagocdf_2.0.0    affyPLM_1.14.0       gcrma_2.10.0
> matchprobes_1.10.0   affy_1.16.0         
> [6] 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
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623