[Bioc-devel] read.AnnotatedDataFrame

[Florian Hahne]

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