Following up on errors when trying to Li Wong method: > > print(data) > AffyBatch object > size of arrays=536x536 features (8982 kb) > cdf=Hu6800 (7129 affyids) > number of samples=4 > number of genes=7129 > annotation=hu6800 > notes= > > class(data) > [1] "AffyBatch" > > test1 <- normalize(data,method="invariantset") > > test1 > AffyBatch object > size of arrays=536x536 features (8982 kb) > cdf=Hu6800 (7129 affyids) > number of samples=4 > number of genes=7129 > annotation=hu6800 > notes= > > test2 <- expresso(data,normalize.method="quantiles",bg.correct=FALSE, > + pmcorrect.method="pmonly",summary.method="liwong") > normalization: quantiles > PM/MM correction : pmonly > expression values: liwong > normalizing...done. > 7129 ids to be processed > .Error in quantile.default(sigma.theta, normal.array.quantile) : > Missing values and NaN's not allowed if `na.rm' is FALSE > In addition: There were 11 warnings (use warnings() to see them) > Error in name.levels(cdf) : Object "cdf" not found THis is odd. Could you do: >data.n <- normalize(data, method="quantiles") >sumis.na(exprs(data.n)) [1] 0 >sum(!is.finite(exprs(data.n)) [1] 0