[BioC] eset from GEOqury pkg

[James F. Reid]

Hi,

I should rectify that I used the GSE approach (ie getGEO("GSE2773")) and 
everything is fine whereas I have just checked again using the GDS 
approach (ie x = getGEO("GDS2248"); y = GDS2eSet(x)) and it does indeed 
return just numbered fvarLabels as you stated.

Best.
J.

On 22/03/12 09:45, James F. Reid wrote:
> Hi,
>
> I cannot replicate this with the current version of R/BioC and with the
> devel one (to be released very soon), i.e I always get the fvarLabels
> (like in your 'old' scenario).
> You didn't provide a sessionInfo() so I do not know what you are using
> and cannot help more.
>
> J.
>
> On 21/03/12 22:43, Jing Huang wrote:
>> Hi Sean,
>>
>> Do you know that eset generated from GDS dataset a few month ago is
>> different from the eset generated now?
>>
>> Old eset:
>>
>>> eset
>> ExpressionSet (storageMode: lockedEnvironment)
>> assayData: 22690 features, 5 samples
>> element names: exprs
>> protocolData: none
>> phenoData
>> sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total)
>> varLabels: sample protocol disease.state description
>> varMetadata: labelDescription
>> featureData
>> featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total)
>> fvarLabels: ID Gene.title ... GO.Component.1 (21 total)
>> fvarMetadata: Column labelDescription
>> experimentData: use 'experimentData(object)'
>> Annotation:
>>
>>
>> New eset:
>>
>>> eset
>> ExpressionSet (storageMode: lockedEnvironment)
>> assayData: 22690 features, 5 samples
>> element names: exprs
>> protocolData: none
>> phenoData
>> sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total)
>> varLabels: sample protocol disease.state description
>> varMetadata: labelDescription
>> featureData
>> featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total)
>> fvarLabels: 1 2 ... 21 (21 total)
>> fvarMetadata: Column labelDescription
>> experimentData: use 'experimentData(object)'
>> Annotation:
>>
>> The difference is in fvarLabels.
>>
>> Could you advise? How to get these names back?
>>
>> Jing
>>
>> OHSU
>>
>>
>> [[alternative HTML version deleted]]
>>
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