Richard Pearson wrote: > Hi Rodrigo > > I think the se.exprs() method disappeared a release or two ago. You can > still get this data by using: > > assayDataElement(eset, "se.exprs") also assayData(eset)[["se.exprs"]], which might have a more familiar feel to it. Both return NULL when se.exprs is not present. Martin > > There are a few methods that I am aware of that give standard errors. In > addition to fitPLM(), I believe you can also get standard errors from > RMA using: > > expresso(affybatch, bgcorrect.method="rma" > , normalize.method="quantiles", pmcorrect.method="pmonly" > , summary.method="medianpolish") > > Also, MBEI (Li and Wong) will give standard errors: > > expresso(affybatch > , normalize.method="invariantset", bg.correct=FALSE > , pmcorrect.method="pmonly", summary.method="liwong") > ) > > My personal recommendation for getting standard errors would be to use > mmgmos() from the package puma (though I might be biased :-) > > You could also look at the function bgx() in the package of the same name > > HTH > > Richard. > > > James W. MacDonald wrote: >> Hi Rodrigo, >> >> Rodrigo Santamar?a Vicente wrote: >>> Hi there!, >>> After performing normalization-summarization with any of the >>> available functions (rma, mas5, plier, etc.), I get an ExpressionSet >>> class. It inherits from eSet class, but it seems to loss the >>> se.exprs() method to get the standard errors for the summarized >>> expression levels. >>> My question is: how could I get the standard errors from the >>> ExpressionSet returned by rma, mas5 or any other method? if these >>> methods do not return standard errors, why? are them unimportant? is >>> there any method that computes them? >> >> None of the methods you mention return standard errors. If you want >> standard errors, you might use the affyPLM package. For instance the >> fitPLM() function will return values very similar to rma(), but with >> standard errors. >> >> Best, >> >> Jim >> >> >>> >>> Thanks in advance! >>> Rodrigo >>> >>> _______________________________________________ >>> 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 >> > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793