Dear All,

I was trying to retrieve GSE record from NCBI GEO using GEOquery package.

The packge was downloaded using
 > gse6901 <- getGEO("GSE6901")

> show(gse6901)

$GSE6901_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 57381 features, 12 samples
  element names: exprs
phenoData
  sampleNames: GSM159259, GSM159260, ..., GSM159270  (12 total)
  varLabels and varMetadata description:
    title: NA
    geo_accession: NA
    ...: ...
    data_row_count: NA
    (35 total)
featureData
  featureNames: AFFX-BioB-3_at, AFFX-BioB-5_at, ..., RPTR-Os-XXU09476-1_at
(57381 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: GPL2025

When i used

 >gsmplatforms <- lapply(GSMList(gse), function(x) {
+ Meta(x)$platform
+ })

It gave me an error

Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "GSMList", for signature
"list"

I checked my R and Bioconductor versions which is as follows, and it seems
fine as they are latest


> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] limma_2.14.6   GEOquery_2.4.5 RCurl_0.9-4    Biobase_2.0.1

I am really not able to understand what is the error and how to solve it and
also how GSE record can be converted into expression record. If anyone has
the solution please let me know. I shall be very thankful.




-- 
Hemant Ritturaj Kushwaha

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