[BioC] IlluminaHumanMethylation27k.db crashes!!

[Vincent Carey]

you can still generate a sessionInfo() before getting into the bad
state.  please do so; otherwise, we do not know what
software configuration is in play.  furthermore, i would suggest using
the terminal to obtain results of "ls -l" on the files
that you imported.

On Thu, May 5, 2011 at 10:05 PM, Jasreet <jovialj86 at gmail.com> wrote:
> @ Sean:
> yes, It is Infinium HumanMethylation27 BeadChip
>
> @Vincent
> There is no error because all i see the mac - rainbow wheel.. And so I end
> up 'force quiting' R without session info.
>
>
> On Thu, May 5, 2011 at 8:44 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>>
>> On Thu, May 5, 2011 at 9:04 PM, Vincent Carey <stvjc at channing.harvard.edu>
>> wrote:
>>>
>>> Please read the posting guide.  What is the error message?  What is
>>> the result of sessionInfo()?
>>>
>>> On Thu, May 5, 2011 at 5:35 PM, Jasreet <jovialj86 at gmail.com> wrote:
>>> > I am new to R and trying to analyze Illumina Infinium Array Data using
>>> > 'lumi' package.
>>> > But whenever I try to load MethylumiM into annotation/color info using
>>> > IlluminaHumanMethylation27k.db , its been crashing consistently!
>>> > Using R for MacOSX.
>>> > Command I used:
>>> >
>>> >>addColorChannelInfo <- lumiMethyR(myFile,
>>> > lib="IlluminaHumanMethylation27k.db")
>>> >
>>> > Here are the contents of the MethyLumiM object :
>>> >>myFile
>>> > MethyLumiM (storageMode: lockedEnvironment)
>>> > assayData: 485577 features, 12 samples
>>
>> And just to be clear, are you sure that you are using a 27k array?  The
>> number of features looks to be something other than a 27k array?
>> Sean
>>
>>>
>>> >  element names: detection, exprs, methylated, unmethylated
>>> > protocolData: none
>>> > phenoData
>>> >  sampleNames: 3y0eY1 3y0eY2 ... 3y0eXY (12 total)
>>> >  varLabels: sampleID label
>>> >  varMetadata: labelDescription
>>> > featureData
>>> >  featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total)
>>> >  fvarLabels: TargetID ProbeID_A ProbeID_B
>>> >  fvarMetadata: labelDescription
>>> > experimentData: use 'experimentData(object)'
>>> >
>>> > Thanks!
>>> > J
>>> >
>>> >        [[alternative HTML version deleted]]
>>> >
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>>
>
>