[BioC] Re: gcrma()/rma() error

[Jose Duarte]

What versions are you on? I hadn't had a look at this since my original
posting back in April but having tried again now it seems that the
problem is gone for me using R 1.9.0 and affy 1.4.30.

Cheers

Jose


On Fri, 2004-06-18 at 12:42, Michael Seewald wrote:
> It seems, I found the reason:
> 
> When justGCRMA() is called in a subdirectory that contains the substring
> "GMS_AllLCM-133A_Foo" it does NOT work. When I rename it to
> "GMS_AllLCM-U133A_Foo" it runs fine. The "-" followed by a number is
> apparently interpreted in a special (numerical?) way when justGCRMA reads the
> CEL files from that directory.
> 
> All of that applies only to the non-interactive session, it runs fine in the
> interactive session.
> 
> Best regards,
> Michael
> 
> 
> On Fri, 18 Jun 2004, Michael Seewald wrote:
> 
> >
> > Sorry, I have to correct myself. I just noted that the command fails *ONLY* in
> > the non-interactive environemnt, e.g. when calling a script with "source". It
> > works when I paste the command interactively into the R shell. This means it
> > behaves exactly like Jose described..
> >
> > Best wishes,
> > Michael
> >
> >
> > On Fri, 18 Jun 2004, Michael Seewald wrote:
> >
> > >
> > > Dear Bioconductor people, dear Jean and Rafael,
> > >
> > > I see the same problem as Jose described (see below) with justGCRMA().
> > >
> > > The following (while located in a directory with CEL files) does not work:
> > >
> > > > DATA.A.GCRMA<-justGCRMA(phenoData=pd)
> > > Computing affinities..Done.
> > > Adjusting for optical effect......................Done.
> > > Adjusting for non-specific binding.....................Done.
> > > Normalizing
> > > Calculating Expression
> > > Error in just.gcrma(filenames = filenames, phenoData = phenoData, description
> > > = description,  :
> > >         dimnames applied to non-array
> > >
> > > Splitting the task into two commands works:
> > >
> > > > DATA.A.GCRMA<-justGCRMA()
> > > Computing affinities..Done.
> > > Adjusting for optical effect......................Done.
> > > Adjusting for non-specific binding.....................Done.
> > > Normalizing
> > > Calculating Expression
> > > > phenoData(DATA.A.GCRMA) <- pd
> > >
> > > There seems to be a (non-critical) bug hidden in the code for the phenotypic
> > > data. By the way, doing the same with justRMA in one step works fine.
> > >
> > > Do you need more information for debugging?
> > >
> > > Regards & best wishes,
> > > Michael
> > >