Hello Benilton,
  Great...thanks a lot. Actually I created two sets of data using affy and
using oligo. But didn't know that fitProbeLevelModel doesn't work with both
the data.
And being new in BioC couldn't recognize the problem with the error
message.
Thanks a lot,
Suparna.


On 5 September 2012 11:26, Benilton Carvalho <beniltoncarvalho@gmail.com>wrote:

> Your code suggests you're using oligo to run the PLM. However, the
> error suggests that you read your data using the affy package, which
> does not create objects compatible with oligo.
>
> Read your data using oligo... then everything should work as expected.
>
> library(oligo)
> InVivodat = read.celfiles(list.celfiles())
> plm = fitProbeLevelModel(InVivodat)
>
>
> best,
> b
>
> On 5 September 2012 11:20, suparna mitra <smitra@liverpool.ac.uk> wrote:
> > Hello Group,
> >   Again problem with "hugene10stv1". After  I installed hugene10stv1cdf
> but
> > now I was trying something again and with Jim's suggestion when I tried :
> >
> >> plm <- fitProbeLevelModel(InVivodat)Loading required package:
> hugene10stv1
> >
> > Error in getProbeInfo(object, target = target, field = vars, sortBy =
> > "man_fsetid",  :
> >
> >   The annotation package 'hugene10stv1' is not available.
> >
> > In addition: Warning message:
> >
> > In library(package, lib.loc = lib.loc, character.only = TRUE,
> > logical.return = TRUE,  :
> >
> >   there is no package called ‘hugene10stv1’
> >
> > though I have hugene10stv1cdf  installed still it wants "hugene10stv1",
> > which I can't find any where.
> >
> >> biocLite("hugene10stv1")
> >
> > BioC_mirror: http://bioconductor.org
> >
> > Using R version 2.15, BiocInstaller version 1.4.7.
> >
> > Warning: unable to access index for repository
> >
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> >
> > Installing package(s) 'hugene10stv1'
> >
> > Warning: unable to access index for repository
> >
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> >
> > Warning: unable to access index for repository
> >
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> >
> > Warning message:
> >
> > package ‘hugene10stv1’ is not available (for R version 2.15.1)
> >
> > Can anybody please help.
> >
> > Best wishes,
> >
> > Suparna
> >
> >         [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Dr. Suparna Mitra
Wolfson Centre for Personalised Medicine
Department of Molecular and Clinical Pharmacology
Institute of Translational Medicine University of Liverpool
Block A: Waterhouse Buildings,  L69 3GL Liverpool

Tel.  +44 (0)151 795 5394, Internal ext: 55394
M: +44 (0) 7511387895
Email id: smitra@liverpool.ac.uk
Alternative Email id: suparna.mitra.sm@gmail.com

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