[BioC] package ‘hugene10stv1’ is not available: problem in fitProbeLevelModel

[Benilton Carvalho]

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 at 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
>
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>
>
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