On Mon, Apr 26, 2010 at 9:58 AM, Kalai Vani <kalai_gene@yahoo.co.in> wrote:

> Dear Sir,
>
> I could perform the GEOquery for  sample data mentioned in your
> PDF, GSE2553
> when I perform the same for another data set 'GSE5764 in GEO
>
> I get the out put of the sample data set performed before.
>
> what is my mistake sir.
>
> gse <- getGEO("GSE5764")
> (gse[[1]])
> dat <- exprs(gse[[1]])
>
> what should i do if  I need to download a new dataset from GEO.
>
>
> *Error* in validObject(.Object) :
>   invalid class "ExpressionSet" object: featureNames differ between
> assayData and featureData
> In addition: Warning message:
> closing unused connection 3
> (C:\Users\rsgk\AppData\Local\Temp\Rtmp6p5q06/GSE5764_series_matrix.txt.gz)
>
>
Hello, Kalaivani.  This works fine for me using a recent version of
GEOquery.  Perhaps you need to upgrade, as I think this issue has been
fixed.  Just as an aside, please be sure to email the bioconductor list, as
this gives you the best chance of getting correct answers.  Also, be sure to
include the output of sessionInfo() with any emails to the list.

Sean


> gse <- getGEO('GSE5764')
Found 1 file(s)
GSE5764_series_matrix.txt.gz
trying URL '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE5764/GSE5764_series_matrix.txt.gz
'
ftp data connection made, file length 3154972 bytes
opened URL
==================================================
downloaded 3.0 Mb

File stored at:
/var/folders/zz/zzzivhrRnAmviuee+++b3E++7lI/-Tmp-//RtmpdfU4SN/GPL570.soft
> gse[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 30 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM134584, GSM134586, ..., GSM134710  (30 total)
  varLabels and varMetadata description:
    title: NA
    geo_accession: NA
    ...: ...
    data_row_count: NA
    (36 total)
featureData
  featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at  (54675 total)
  fvarLabels and fvarMetadata description:
    ID: NA
    GB_ACC: NA
    ...: ...
    Gene.Ontology.Molecular.Function: NA
    (16 total)
  additional fvarMetadata: Column, Description
experimentData: use 'experimentData(object)'
Annotation: GPL570
> validObject(gse[[1]])
[1] TRUE
> sessionInfo()
R version 2.11.0 Under development (unstable) (2009-11-03 r50304)
x86_64-apple-darwin

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] GEOquery_2.11.3 RCurl_1.4-1     bitops_1.0-4.1  Biobase_2.7.6

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