[Bioc-devel] fData(x) <- gives errors for ExpressionSet objects

[Martin Morgan]

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 at 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
>
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-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
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