Hi, My cDNA array have 2 duplicate for each spot. I read and normalize my data set in limma. I use the result MAList (MA) object in timecourse package. But, I get a error: > out1 <- mb.long(MA.2, times = 3, reps = size) Time group assignments are set to default. Replicate group assignments are set to default. Erro em mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, time.grp, : 890 genes may have missing values in some of the replicates. If I use method="normexp" in backgroundCorrect function in limma, the error disappear. But, I would like to use the method="subtract". Do timecourse package handle NAs? In this array I have controls (DMSO and spike, around 1000 spots) and I flagged they, then I use wt.fun=function(x) as.numeric(x$Flag==0) to exclude they in read.maimages function. Could you advice me to solve this problem, if it is possible to solved? Thank you very much -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526

Hi Marcelo, The current timecourse package only deals with missing replicates, but not any missing value within any replicate. So if a whole replicate is a vector of NA, then it should be fine as long as you have at least 2 non-NA replicated vectors. But if within a replicate vector, some of the values are NA, then it doesn't work. Yu Chuan > Hi, > > My cDNA array have 2 duplicate for each spot. > > I read and normalize my data set in limma. > > I use the result MAList (MA) object in timecourse package. > > But, I get a error: > >> out1 <- mb.long(MA.2, times = 3, reps = size) > Time group assignments are set to default. > Replicate group assignments are set to default. > Erro em mb.1D(object, times, reps, prior.df, prior.COV, prior.eta, time.grp, : > 890 genes may have missing values in some of the replicates. > > If I use method="normexp" in backgroundCorrect function in limma, the > error disappear. But, I would like to use the method="subtract". Do > timecourse package handle NAs? > > In this array I have controls (DMSO and spike, around 1000 spots) and > I flagged they, then I use wt.fun=function(x) as.numeric(x$Flag==0) to > exclude they in read.maimages function. > > Could you advice me to solve this problem, if it is possible to solved? > > Thank you very much > > -- > Marcelo Luiz de Laia > Ph.D Candidate > S?o Paulo State University (http://www.unesp.br/eng/) > School of Agricultural and Veterinary Sciences > Department of Technology > Via de Acesso Prof. Paulo Donato Castellane s/n > 14884-900 Jaboticabal - SP - Brazil > Phone: +55-016-3209-2675 > Cell: +55-016-97098526 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >