[BioC] LIMMA No residual using rmaPLM

[Ben Bolstad]

I'd recommend that you use fitPLM rather than rmaPLM for these purposes.
The reason why it is giving "reasonable results" in the first case and
an error in the other case, is that it is using your user supplied
weights in the earlier situation and trying to derive some sensible
weights based on the PLM model fit. Unfortunately rmaPLM does not return
the information that is used to construct these but fitPLM does.

Ben

On Mon, 2005-09-05 at 13:51 +0300, Ron Ophir wrote:
> Hi
> I am analyzing affymetrix data having the following experimental
> design:
> > analysis$design
>                 Normal IOP IOPC
> L91RAE230 2.CEL      0   1    0
> L92RAE230 2.CEL      0   1    0
> L93RAE230 2.CEL      0   0    1
> L94RAE230 2.CEL      0   0    1
> L95RAE230 2.CEL      1   0    0
> L96RAE230 2.CEL      1   0    0
>  and following contrasts
> > analysis$contrasts
>        IOPC.IOP IOPC.Normal IOP.Normal
> Normal        0          -1         -1
> IOP          -1           0          1
> IOPC          1           1          0
> The preprocessing was done using affyPLM packge
> analysis$data<-rmaPLM(analysis$raw)
> where analysis$raw is AfyyBatch object. Then I fitted the the model
> once with weighting matrix using AMP flags
> fm<-as.matrix(analysis$Flags!="A")
> analysis$fit<-lmFit(analysis$data,analysis$design,w=matrix(as.numeric(fm),dim(fm)[1],dim(fm)[2],dimnames=dimnames(fm)))
>   and got a reasonable results and once without this matrix. What was
> surprising is that fitting without the weighting matrix I got the
> following error message:
> > analysis$bayes<-eBayes(analysis$contrasts.fit)
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) : 
>         No residual degrees of freedom in linear model fits
> I've checked the fit coeffecient matrix (analyis$fit object) and is all
> NA.
> Does someone have an idea why? I did not applied any weighting matrix
> for this fitting.
> Thanks
> Ron
> 
> 
>  
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor