[BioC] biobase phenodata

[Sean Davis]

On Mon, Sep 8, 2008 at 3:08 PM, hemant ritturaj
<ritturajhemant at gmail.com> wrote:
> Dear Sean
>
> Thanks for the reply
>
> I tried the way you have suggested but again it gave me an error
>
> gse6901.eset <- getGEO("GSE6901")[[1]]
>
>
> Error in validObject(.Object) :
>   invalid class "ExpressionSet" object: featureNames differ between
> assayData and featureData
>
> Check the version of R and other packges which are updated to newer version

Hemant,

I'm not sure what the problem is.  This works fine for me (see
sessionInfo below).  If you quit R and restart it with an empty
workspace and execute the following, do you get the same error?

Sean

----------------------------------------------------
> library(GEOquery)
> gse <- getGEO('gse6901')[[1]]
> gse
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_a
  t  (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

> sessionInfo()
R version 2.7.2 (2008-08-25)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

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



> On Tue, Sep 9, 2008 at 12:52 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>
>> On Mon, Sep 8, 2008 at 2:37 PM, hemant ritturaj
>> <ritturajhemant at gmail.com> wrote:
>> > Dear all,
>> >
>> > I was trying to make expression set from the GSE data
>>
>> This will get you an ExpressionSet:
>>
>> gse6901.eset <- getGEO("GSE6901")[[1]]
>>
>> Now, gse6901.eset is an ExpressionSet.  No need for all the code
>> below.  The [[1]] is needed because getGEO() on a GSEMatrix returns a
>> list of ExpressionSets.  In this particular case, there is only one
>> ExpressionSet, so we choose it.
>>
>> Sean
>>
>> > Following is the code
>> >
>> > gse6901 <- getGEO("GSE6901", GSEMatrix=F)
>> > probesets <- Table(GPLList(gse6901)[[1]])$ID
>> > data.matrix <- log2(do.call("cbind", lapply(GSMList(gse6901),
>> > function(x) {
>> > + tab <- Table(x)
>> > + mymatch <- match(probesets, tab$ID_REF)
>> > + return(as.numeric(tab$VALUE[mymatch]))
>> > + })))
>> > rownames(data.matrix) <- probesets
>> > colnames(data.matrix) <- names(GSMList(gse6901))
>> > pdata <- data.frame(samples = names(GSMList(gse6901)))
>> > rownames(pdata) <- names(GSMList(gse6901))
>> > pheno <- new("phenoData", pData = pdata, varLabels = as.list("samples"))
>> >
>> >
>> > Error: The phenoData class is defunct, use AnnotatedDataFrame (with
>> > ExpressionSet) instead
>> >
>> > I am not able to understand what function has exactly gor changed in
>> > Biobase
>> > module as I tried
>> >
>> > pheno <- new("AnnotatedDataFrame", pData = pdata, varLabels =
>> > as.list("samples"))
>> >
>> > then again got an error
>> >
>> > Error in .nextMethod(.Object, ...) :
>> >  invalid names for slots of class "AnnotatedDataFrame": pData, varLabels
>> >
>> > Kindly anyone please help me sorting out this error, I shall be very
>> > thankful for your kind help
>> >
>> > Regards
>> > --
>> > Hemant Ritturaj Kushwaha
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>
>
>
>