On Wed, May 07, 2003 at 12:54:42PM -0600, Ann Hess wrote: > Here is what I got: > > > immediately before the call to expresso that gives errors try > > > > 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)) sum(!is.finite(exprs(data.n)) > > > warnings() > Warning messages: > 1: No convergence achieved in outlier loop > in: fit.li.wong(probes, ...) > 2: No convergence achieved in outlier loop > in: fit.li.wong(probes, ...) > > > > ps the non convergence warning is something you have to live with when > > using li and wongs method. sometimes their algorithm doesnt converge. its > > usually a very small percentage of the probesets though. note: the devel version of the pack returns the genes for which a problem occurred (associated attribute). > > ***OK, but the call doesn't seem to return anything: > > exprs(eset)[1:100,] > Error in exprs(eset) : Object "eset" not found > ***OR > > test2 > Error: Object "test2" not found > This is normal. An error interrupted the 'making' of the eset in the middle. L. > > > > > On Wed, 7 May 2003, Ann Hess wrote: > > > > > I am trying to use the expresso command to get MBEI values. I get the > > > following errors. Note that I was able to use expresso to get RMA and MAS > > > values for the same data without any errors. Any suggestions? > > > > > > **I am using R version 1.6.2 and affy version 1.1.1. > > > > > > > eset3<-expresso(data,normalize.method="invariantset",bg.correct=FALSE, > > > pmcorrect.method="pmonly",summary.method="liwong") > > > > > > normalization: invariantset > > > 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: Warning messages: > > > 1: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 2: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 3: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 4: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 5: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > Error in name.levels(cdf) : Object "cdf" not found > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

ps - the next release (the devel version as well) will continue despite the error and give you back an exprSet with values for the probesets were the algorithm worked. attributes(eset3)$pps.warnings contains info on probesets that gave problems in version 1.1.1 you can run expresso and send all probenames, except the problemtic ones, using the summary.subset argument. On Wed, 14 May 2003, Rafael A. Irizarry wrote: > it turns out the HU6800 array has two probesets > with just one probe pair: > > "HG2887-HT3031_at" > "U90546_r_at" > > in this case the li and wong algorithm, as implemented in the affy > package, wont work. the li and wong model doesnt really apply. hopefully > the next release will incorporate a warning about this. > > > On Wed, 7 May 2003, Ann Hess wrote: > > > > > I am trying to use the expresso command to get MBEI values. I get the > > > following errors. Note that I was able to use expresso to get RMA and MAS > > > values for the same data without any errors. Any suggestions? > > > > > > **I am using R version 1.6.2 and affy version 1.1.1. > > > > > > > eset3<-expresso(data,normalize.method="invariantset",bg.correct=FALSE, > > > pmcorrect.method="pmonly",summary.method="liwong") > > > > > > normalization: invariantset > > > 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: Warning messages: > > > 1: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 2: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 3: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 4: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > 5: No convergence achieved in outlier loop > > > in: fit.li.wong(probes, ...) > > > Error in name.levels(cdf) : Object "cdf" not found > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > > >