Dear Bioconductor: I ran expresso with the estrogen data set on R2.1.0 (affy 1.5.8-1)installed on Windows XP. Normalization with qspline worked fine, but not with loess. Any suggestions? > x <- expresso(data_cel, bgcorrect.method="rma", + normalize.method="qspline", + pmcorrect.method="pmonly", + summary.method="medianpolish") background correction: rma normalization: qspline PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...[1] "samples= 404 k= 5 first= 999" . .. . done. 12625 ids to be processed | | |####################| > y <- expresso(data_cel, bgcorrect.method="rma", + normalize.method="loess", + pmcorrect.method="pmonly", + summary.method="medianpolish") background correction: rma normalization: loess PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...Error: NA/NaN/Inf in foreign function call (arg 1) Any comments will be appreciated! Jianping Jin

Jianping Jin <jjin@email.unc.edu> writes: > Dear Bioconductor: > > I ran expresso with the estrogen data set on R2.1.0 (affy 1.5.8-1)installed > on Windows XP. Normalization with qspline worked fine, but not with loess. > Any suggestions? Try the devel version of affy. The current Bioc 1.5 release is not compatible with R 2.1.0. + seth

Dear BioC: I used expresso to get expression values with the summary.method="medianpolish". I am wondering if the resulting values are in log base 2? Do the other methods, such as bgcorrect.method and normalize.method, also determine the output value in regular numeric or log form? thanks! Jianping Jin xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin@email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Medianpolish is in in log base 2. Many of the others are in regular numeric. Alexander Cambon Biostatistics and Bioinformatics University of Louisville >>> Jianping Jin <jjin@email.unc.edu> 5/11/2005 5:12:23 PM >>> Dear BioC: I used expresso to get expression values with the summary.method="medianpolish". I am wondering if the resulting values are in log base 2? Do the other methods, such as bgcorrect.method and normalize.method, also determine the output value in regular numeric or log form? thanks! Jianping Jin xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin@email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor