Dear all, I got this error while I was trying to normalize (first within arrays, then between arrays) Agilent arrays using these code lines (R2.0.0, bioConductor 1.5, Windows XP): > #########normalize within arrays > MA<-normalizeWithinArrays(RG, method="loess", bc.method="normexp", > offset=2) Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Corrected array 5 Corrected array 6 Corrected array 7 Corrected array 8 Corrected array 9 Corrected array 10 Corrected array 11 Corrected array 12 Corrected array 13 Corrected array 14 Corrected array 15 Corrected array 16 Corrected array 17 Corrected array 18 Corrected array 19 Corrected array 20 Corrected array 21 Corrected array 22 Corrected array 23 Corrected array 24 > > #########normalize between arrays > MA.b=normalizeBetweenArrays(MA, method="quantile") Error in xy.coords(x, y) : x and y lengths differ I found that MA$A and MA$M contain a few columns with all "NA" values. if I replace bc.method="normexp" with bc.method="half", everything look fine. if I did not use the "bg.method" option at all, then many elements (but not all) of the columns metioned above (all "NA") are "NA". Thanks Caimiao

>Date: Wed, 17 Nov 2004 15:32:39 -0800 >From: "Caimiao Wei" <caimiaow@u.washington.edu> >Subject: [BioC] error in Limma normalization with bc.method="normexp" >To: <bioconductor@stat.math.ethz.ch> > > Dear all, > >I got this error while I was trying to normalize (first within arrays, then >between arrays) Agilent arrays using these code lines (R2.0.0, bioConductor >1.5, Windows XP): > > > #########normalize within arrays > > > MA<-normalizeWithinArrays(RG, method="loess", bc.method="normexp", > > offset=2) >Corrected array 1 >Corrected array 2 >Corrected array 3 >Corrected array 4 >Corrected array 5 >Corrected array 6 >Corrected array 7 >Corrected array 8 >Corrected array 9 >Corrected array 10 >Corrected array 11 >Corrected array 12 >Corrected array 13 >Corrected array 14 >Corrected array 15 >Corrected array 16 >Corrected array 17 >Corrected array 18 >Corrected array 19 >Corrected array 20 >Corrected array 21 >Corrected array 22 >Corrected array 23 >Corrected array 24 > > > #########normalize between arrays > > > MA.b=normalizeBetweenArrays(MA, method="quantile") >Error in xy.coords(x, y) : x and y lengths differ > >I found that MA$A and MA$M contain a few columns with all "NA" values. This is almost certainly an indication that the "normexp" algorithm has failed for those arrays. The "normexp" algorithm uses a Nelder-Mead derivative-free optimisation method. It works most of the time but not on all data sets. I do not have a fix at this stage. Sorry. You'll need to stick with bg.method="half". In general you should check you have no missing values before using normalizeBetweenArrays() with method="quantile". Gordon >Thanks >Caimiao