Dear All, I am trying to single channel analysis for my data and i get "In remlscore(y, X, Z) : reml: Max iterations exceeded" this error. I did not get this error before and i was trying to reanalyze this data and encounter this error. I also updated Statmod package but still get this error. I appreciate any help in this regard. Here are the commands list : targets<-readTargets("targets.txt") > RG<-read.maimages(targets,source="genepix",wt.fun=wtflags(weight=0),co lumns=list(R="F635 Median",G="F532 Median",Rb="B635",Gb="B532")) Read 13961538.gpr Read 13961556.gpr Read 13961428-2.gpr Read 13961652.gpr Read 13961645.gpr Read 13961646.gpr Read 13961649.gpr Read 13961635.gpr Read 13961661.gpr Read 13961800.gpr > RG$genes<-readGAL() > spottypes<-readSpotTypes("Spottypes.txt") > RG <- backgroundCorrect(RG, method="normexp", offset=50) Green channel Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Corrected array 5 Corrected array 6 Corrected array 7 Corrected array 8 Corrected array 9 Corrected array 10 Red channel Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Corrected array 5 Corrected array 6 Corrected array 7 Corrected array 8 Corrected array 9 Corrected array 10 > MA <- normalizeWithinArrays(RG) > MA.Aq<-normalizeBetweenArrays(MA,method="Aquantile") > > targets2<-targetsA2C(targets) > targets2 channel.col SlideNumber FileName Identity Target 1.1 1 13961538 13961538.gpr RAO103 RT30 1.2 2 13961538 13961538.gpr RAO103 RT0 2.1 1 13961556 13961556.gpr RAO61 RT30 2.2 2 13961556 13961556.gpr RAO61 RT0 3.1 1 13961428 13961428-2.gpr RAO40 RT30 3.2 2 13961428 13961428-2.gpr RAO40 RT0 4.1 1 13961652 13961652.gpr RAO123 RT0 4.2 2 13961652 13961652.gpr RAO123 RT30 5.1 1 13961645 13961645.gpr RAO306 RT0 5.2 2 13961645 13961645.gpr RAO306 RT30 6.1 1 13961646 13961646.gpr RAO312 RT0 6.2 2 13961646 13961646.gpr RAO312 RT30 7.1 1 13961649 13961649.gpr Con32 CT30 7.2 2 13961649 13961649.gpr Con32 CT0 8.1 1 13961635 13961635.gpr Con53 CT30 8.2 2 13961635 13961635.gpr Con53 CT0 9.1 1 13961661 13961661.gpr Con87 CT0 9.2 2 13961661 13961661.gpr Con87 CT30 10.1 1 13961800 13961800.gpr Con106 CT0 10.2 2 13961800 13961800.gpr Con106 CT30 > u<-unique(targets2$Target) > f<-factor(targets2$Target,levels=u) > design<-model.matrix(~0+f) > colnames(design)<-u > corfit<-intraspotCorrelationMA.Aq,design) Loading required package: statmod Warning messages: 1: In remlscore(y, X, Z) : reml: Max iterations exceeded 2: In remlscore(y, X, Z) : reml: Max iterations exceeded Thanks Priyanka [[alternative HTML version deleted]]