[BioC] (GC)RMA estimates without summerization?
Guido.Hooiveld at wur.nl
Mon Feb 11 21:41:37 CET 2008
Thanks Ben, got it working fine for RMA!
Two more questions, though (I hope you don't mind):
- Output of preprocess is an AffyBatch object; how to save the
> esetrma <- preprocess(rawdata)
> write.table(exprs(esetrma), file="RMA_no_summary.tx", sep="\t")
but that produces a huge file, and when viewed it contains both
'normal'and log2 values; the log2-values are obviously the expression
estimates, but what are the 'normal' values? These are likely not
needed. And how to put the probe ID in the first column, i.e. how to
list the expression estimates per probe?
- I would like to apply the emperical Bayes estimate for bakcground
correction of GCRMA in stead of the miximum likelyhood estimate (MLE).
Normally you would do this by specifying the argument "FAST=false":
esetgcrma <- gcrma(rawdata, fast=FALSE)
How to do this in preprocess() [or threestep()]? I assume both functions
apply the default settings of gcrma, which is fast=TRUE.
This doesn't work:
> esetgcrma <- preprocess(rawdata, background.method = "GCRMA",
Error in preprocess(rawdata, background.method = "GCRMA", fast = FALSE)
unused argument(s) (fast = FALSE)
> -----Original Message-----
> From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com]
> Sent: 11 February 2008 19:56
> To: Hooiveld, Guido
> Subject: Re: [BioC] (GC)RMA estimates without summerization?
> Try preprocess() in affyPLM, it should allow you to do
> anything that you can do with threestep() except the
> summarization step.
> > 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:
> >  splines tools stats graphics grDevices utils
> > 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]]
> > _______________________________________________
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