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"
> 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
--
===================================
anjan purkayastha, phd.
research associate
fas center for systems biology,
harvard university
52 oxford street
cambridge ma 02138
phone-703.740.6939
===================================
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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
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