[BioC] Simpleaffy problems

[James W. MacDonald]

Hi Anjan,

Two things;

First, please don't reply to me alone. The list archives are intended to 
be a searchable resource of questions and answers.

Second, you didn't send me the output of sessionInfo(). However, the 
matchprobes warning below indicates you are using BioC 2.4, which is 
ancient in the context of R/BioC (we are at release 2.6, and will soon 
release 2.7). We are not able to give support to previous releases, so 
please update to 2.6 and try again.

Best,

Jim



On 10/4/2010 4:47 PM, ANJAN PURKAYASTHA wrote:
> Hi Jim,
> Thanks for your feedback.
> This time I loaded only simpleaffy. Output:
> Loading required package: affy
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'openVignette()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: genefilter
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: AnnotationDbi
> Loading required package: Biostrings
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
>
>      The following object(s) are masked from package:Biobase :
>
>       annotation,
>       annotation<-
>
>
>      The following object(s) are masked from package:base :
>
>       cbind,
>       order,
>       pmax,
>       pmax.int,
>       pmin,
>       pmin.int,
>       rbind,
>       rep.int,
>       table
>
>
> *** Deprecation warning ***
> The matchprobes package is deprecated and will not be supported
> after Bioconductor release 2.4. Please switch to using the Biostrings
> package for efficient string manipulations. If you need to build a
> probe package, please see the makeProbePackage vignette in the
> AnnotationDbi package.
>
>
> Attaching package: 'simpleaffy'
>
>
>      The following object(s) are masked _by_ .GlobalEnv :
>
>       getBioC
>
>
> Next, I created an Affybatch object: mtbH0h and plugged in the command:
> mtbH0h.quality<- qc(mtbH0h)
>
> which gives me the error output:
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "annotation", for
> signature "AffyBatch"
>
> Any idea where I am making an error?
> Thanks in advance!
> Anjan
>
> On Tue, Sep 28, 2010 at 8:58 AM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
>
>> Hi Anjan,
>>
>>
>> On 9/27/2010 4:38 PM, ANJAN PURKAYASTHA wrote:
>>
>>> So, I want to run some QC on an Affy data set- data0hR.
>>> Shown are my commands and the errors thrown by simpleaffy:
>>>
>>>> library(simpleaffy)
>>>>
>>>
>>>   data0hR.qc<- qc(data0hR)
>>>>
>>> Error in function (classes, fdef, mtable)  :
>>>    unable to find an inherited method for function "annotation", for
>>> signature "AffyBatch"
>>>
>>
>> I don't see a call to annotation() in the qc() function from simpleaffy, so
>> I wonder if you are masking with another function from another package?
>>
>> Will you try again with only simpleaffy loaded, and send us the output of
>> sessionInfo()?
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>
>>>   avbg(data0hR.qc)
>>>>
>>> Error: object 'data0hR.qc' not found
>>> Error in avbg(data0hR.qc) :
>>>    error in evaluating the argument 'object' in selecting a method for
>>> function 'avbg'
>>>
>>> I use R on a Mac OS X 10.5.8.
>>> Any helpful feedback will be appreciated.
>>> Thanks,
>>> Anjan
>>>
>>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues