[BioC] eset from GEOqury pkg

[Jing Huang]

Many thanks Sean.

Jing

-----Original Message-----
From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis
Sent: Thursday, March 22, 2012 4:29 AM
To: Jing Huang
Cc: bioconductor at r-project.org
Subject: Re: [BioC] eset from GEOqury pkg

On Wed, Mar 21, 2012 at 6:43 PM, Jing Huang <huangji at ohsu.edu> wrote:
> Hi Sean,
>
> Do you know that eset generated from GDS dataset a few month ago is different from the eset generated now?

Thanks, Jing, for the bug report.  This is fixed in 2.20.9 and 2.21.9
(release and devel) and should be available in a day or two.

Sean



> 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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>
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