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@wur.nl 

 

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