[BioC] eset from GEOqury pkg

[James F. Reid]

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
>
>
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