[BioC] Spot duplicate in timecourse package and "missing" values

[Yu Chuan Tai]

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
> São 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
>