[Bioc-devel] read.AnnotatedDataFrame

[Martin Morgan]

Thanks Florian -- oddly, Crispin Miller sent email earlier today about
this same issue; it's fixed in R-devel. 

read.AnnotatedDataFrame was introduced to accommodate modifications to
affy; is this (affy) where the problem came from? I'm not really sure
how people get info into ExpressionSets, and would be happy to make
that process easier / more robust.

Martin

Florian Hahne <f.hahne at dkfz-heidelberg.de> writes:

> Hi Martin, all
>
> I tried to adopt the read.AnnotatedDataFrame method on files that I was
> able to import with read.phenoData before and got the following error
> message:
>
> Error in data.frame(labelDescription = varLabels, row.names =
> names(varLabels)) :
>         row names supplied are of the wrong length
>
> After taking a look at the code and changing the line
>     varLabels <- as.list(rep("read from file", ncol(pData)))
> to
>     varLabels <- rep("read from file", ncol(pData))
> the function created the AnnotatedDataFrame
>
> Not sure if this is a bug or if my phenoData files should be formated in
> another way, but I strongly doubt that the original version will work in
> any case, since the implicit coercion in the following
> varMetadata = data.frame(labelDescription = varLabels,
>                 row.names = names(varLabels))))
> creates a data frame with 1 row and length(varLabels) columns, hence the
> row.names=names(varLabels) argument will cause an error.
>
> Am i wrong here?
> Florian
>
>
>  sessionInfo()
> R version 2.5.0 Under development (unstable) (2006-05-24 r38188)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=de_DE.ISO-8859-1;LC_NUMERIC=C;LC_TIME=de_DE.ISO-8859-1;LC_COLLATE=de_DE.ISO-8859-1;LC_MONETARY=de_DE.ISO-8859-1;LC_MESSAGES=de_DE.ISO-8859-1;LC_PAPER=de_DE.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.ISO-8859-1;LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] "splines"   "grid"      "tools"     "methods"   "stats"     "graphics"
>  [7] "grDevices" "utils"     "datasets"  "base"
>
> other attached packages:
>   genefilter     survival    rnaiUtils      flomisc        RODBC       
> prada
>     "1.13.5"       "2.29"        "1.0"      "1.0.2"      "1.1-7"    
> "1.11.3"
> RColorBrewer      Biobase
>      "0.2-3"    "1.13.29"
>
>
>
> -- 
> Florian Hahne
> Abt. Molekulare Genomanalyse (B050)
> Deutsches Krebsforschungszentrum (DKFZ)
> Im Neuenheimer Feld 580
> D-69120 Heidelberg
> phone: 0049 6221 424764
> fax: 0049 6221 423454
> web: www.dkfz.de/mga
>

-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org