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List:       bioc-devel
Subject:    Re: [Bioc-devel] fData(x) <- gives errors for ExpressionSet objects
From:       Gordon Smyth <smyth () wehi ! EDU ! AU>
Date:       2007-11-01 6:00:25
Message-ID: 6.2.5.6.1.20071101165528.02f69e60 () wehi ! edu ! au
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Martin,

Thanks, upgrading to Biobase 1.16.1 fixes this and other problems.

Cheers
Gordon

At 04:40 PM 1/11/2007, Martin Morgan wrote:
> Thanks Gordon for the report.
> 
> I think the row names being objected to are the varMetadata row names
> (only two of them), rather than the pData row names. More importantly,
> I think this was fixed in Biobase 1.16.1, on October 15 (reported by
> Richard Pearson around that time).
> 
> Sorry for the inconvenience; if there are other problems, or this is
> not addressed in the patch, then please let me know.
> 
> Martin
> 
> Gordon Smyth <smyth@wehi.EDU.AU> writes:
> 
> > I've a lot trouble adding information to the featureData of
> > ExpressionSet objects. Here is a small reproducible example which
> > shows up one error message.
> > 
> > > library(Biobase)
> > > example(ExpressionSet)
> > 
> > > fData(expressionSet)
> > NULL data frame with 500 rows
> > > df <- data.frame(a=1:500,b=1:500)
> > > rownames(df) <- featureNames(expressionSet)
> > > eS <- expressionSet;
> > > all.equal(row.names(fData(eS)),row.names(df))
> > [1] TRUE
> > > fData(eS) <- df
> > 
> > This all seems good so far. I've been able to overwrite the pData()
> > data.frame. But suppose I add a column first. It shouldn't make any
> > difference, but now replacing the data.frame now longer works. The
> > error complains about row.names, but these are still apparently correct.
> > 
> > Gordon
> > 
> > > eS <- expressionSet
> > > fData(eS)$Number <- 1:500
> > > all.equal(row.names(fData(eS)),row.names(df))
> > [1] TRUE
> > > fData(eS) <- df
> > Error in `row.names<-.data.frame`(`*tmp*`, value = c("a", "b")) :
> > invalid 'row.names' length
> > 
> > > sessionInfo()
> > R version 2.6.0 (2007-10-03)
> > i386-pc-mingw32
> > 
> > locale:
> > 
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
> 
> > 
> > attached base packages:
> > [1] tools     stats     graphics  grDevices
> > utils     datasets  methods   base
> > 
> > other attached packages:
> > [1] Biobase_1.16.0
> > 
> > _______________________________________________
> > Bioc-devel@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> --
> Martin Morgan
> Computational Biology Shared Resource Director
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793

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