[Bioc-devel] read.AnnotatedDataFrame

[Martin Morgan]

Martin Morgan <mtmorgan at fhcrc.org> writes:

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

Sorry, meant that it was fixed in the development version of
Biobase. Martin


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