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

[Benilton Carvalho]

Please, don't take discussion off the list. I'm cc-ing bioc, so others
can benefit from the discussion.

Because you didn't post the results of sessionInfo() as recommended,
I'm just guessing... It looks like you've got both oligo and affy
loaded simultaneously. Then what's probably happening is that the
rma() defined in affy in taking precedence...

If you use fully qualified names, as in:

rmaOligo = oligo::rma(InVivodat1)

it *should* work.

My recommendation is: if you must have results by both oligo and affy,
do this in different sessions. It makes things simpler, as you don't
need to worry with such details.

b


On 5 September 2012 12:00, suparna mitra <smitra at liverpool.ac.uk> wrote:
> Hello Benilton,
>   Yes now the fitProbeLevelModel works with my 2nd set data created using
> read.celfiles but somehow I am having problem to use this data for
> normalization. Where as first set data created using ReadAffy works great
> for normalization.
>
>> plm <- fitProbeLevelModel(InVivodat1)
>
> Background correcting... OK
>
> Normalizing... OK
>
> Summarizing.... OK
>
> Extracting...
>
>   Estimates... OK
>
>   StdErrors... OK
>
>   Weights..... OK
>
>   Residuals... OK
>
>   Scale....... OK
>
>> eset.invivo1=rma(InVivodat1)
>
> Error in function (classes, fdef, mtable)  :
>
>   unable to find an inherited method for function "probeNames", for
> signature "GeneFeatureSet"
>
> But with the other data
>
>> eset.invivo=rma(InVivodat)
>
> Background correcting
>
> Normalizing
>
> Calculating Expression
>
>> write.exprs(eset.invivo, file="InVivodata.txt")
>
> Can you suggest any fix fo this?
> Thanks a lot,
> Suparna.
>
>
> On 5 September 2012 11:44, suparna mitra <smitra at liverpool.ac.uk> wrote:
>>
>> 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 at 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 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
>>> >
>>> >         [[alternative HTML version deleted]]
>>> >
>>> >
>>> > _______________________________________________
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>>
>>
>>
>>
>> --
>> 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 at liverpool.ac.uk
>> Alternative Email id: suparna.mitra.sm at gmail.com
>>
>
>
>
> --
> 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 at liverpool.ac.uk
> Alternative Email id: suparna.mitra.sm at gmail.com
>