[BioC] Error in AnnBuilder writeAnnData2Pkg

[John Zhang]

I believe that in your base file there was a line with "" for probe and ACC ids. 
Remove the first row of annotation (annotation <- 
annotation[2:nrow(annotation),]) and try the code again.

>Here are the first two lines of the annotation matrix. For reasons that  
>I do not understand, the first line is empty. Could this be the reason  
>for the error? And is there a way to circumvent this?
>
> > annotation[1:2,]
>                     PROBE                 ACCNUM     LOCUSID UNIGENE
>                     ""                    ""         "NA"    "NA"
>CGENZEB_456000002_0 "CGENZEB_456000002_0" "AF030031" "30131" "Dr.30326"
>                     GENENAME SYMBOL CHR  MAP  PMID                       
>    GRIF
>                     "NA"     "NA"   "NA" "NA" "NA"                       
>    "NA"
>CGENZEB_456000002_0 "deltaA" "dla"  "1"  "NA"  
>"12890499;12835391;12477932" "NA"
>                     SUMFUNC
>                     "NA"
>CGENZEB_456000002_0 "NA"
>                     GO
>                     "NA"
>CGENZEB_456000002_0  
>"GO:0005509 at IEA;GO:0007154 at IEA;GO:0009880 at IMP;GO:0016020 at IEA;GO:0005515@ 
>IDA"
>                     OMIM REFSEQ
>                     "NA" "NA"
>CGENZEB_456000002_0 "NA" "NM_130954;NP_571029"
>
>
>Best,
>
>Georg
>
>
>>
>>>> pkgName<-"test"
>>>> pkgPath<-getwd()
>>>> createEmptyDPkg(pkgName, pkgPath, force=TRUE)
>>>> annotation<-as.matrix(annotation)
>>
>> What did annotation contain? Did annotation have column names? You  
>> need to
>> provide us with more information (e. g. R version, AnnBuilder version,  
>> more
>> example code)
>>
>>
>>>
>>> then I get the following error:
>>>
>>>> writeAnnData2Pkg(annotation, pkgName, pkgPath)
>>>
>>> Error in assign(x[i], value[[i2]], envir = envir, inherits =  
>>> inherits) :
>>>         attempt to use zero-length variable name
>>>
>>>
>>> Could someone give me a hint what is wrong here?
>>>
>>> Best,
>>>
>>> Georg
>>>
>>> P.S. I am on digest mode, cc'ing the answer directly to me would be  
>>> nice
>
>
>
>-- 
>Georg Wilhelm Otto
>Max-Planck-Institute for Developmental Biology
>Spemannstrasse 35/III
>D-72076 Tuebingen Germany
>phone: +49-7071-601 401
>http://www.eb.tuebingen.mpg.de

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084