[BioC] Error in AnnBuilder writeAnnData2Pkg

[Georg Otto]

Thanks a lot, John!

In fact in my base file there were quite a few empty lines that I  
missed. I changed the basefile and now it works.

Best,

Georg

> 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:000551 
>> 5@
>> 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