[BioC] fRMA error when using exprs()

[Sylvain Brohée]

I did not say I found the solution but I reinstalled everything (R, 
Bioconductor and all the packages I needed) and now it seems to work.

Thanks for your help. 

Sylvain Brohée


On Thursday, September 15, 2011 11:48:55 AM Sylvain Brohée wrote:
> Dear all,
> 
> I am quite new to the "affymetrix normalization data world" and until now, I 
> was always normalizing my data using the good old RMA method.
> 
> People in the wet lab I am collaborating with asked me to renormalize a set 
of 
> data coming from different labs and I discovered the fRMA method which is 
> certainly more suitable in that case.
> 
> I am working on the mouse so I used the mouse4302frmavecs package.
> 
> This is my script :
> 
> rawdata <- ReadAffy(filenames = cel.files)
> eset.frma <- frma(rawdata, summarize = 'batch');
> 
> When I run this, everything seems OK (about 5-6 to run) until I run this 
> command :
> 
> eset.df <- exprs(eset.frma);
> 
> which produces the following error 
> 
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "exprs", for signature 
> "PLMset"
> 
> and if I look at my eset.frma object, I get this 
> 
> Probe level linear model (PLMset) object
> size of arrays=1002x1002
> cdf=Mouse430_2 (45101 probeset ids)
> number of samples=6
> number of probesets=45101
> number of chip level parameters for each probeset=6
> annotation=mouse4302
> PLMset settings
> Creating function: 
> Preprocessing
> Background Correction=Error in if 
> (object at model.description$preprocessing$background) { : 
>   argument is of length zero
> 
> 
> The only thing I'd like are the expression values of course. 
> 
> Any idea about the cause of the problem?
> 
> Many thanks to all of you,
> 
> Sylvain Brohée
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
http://news.gmane.org/gmane.science.biology.informatics.conductor
>