[BioC] illumina annotation package error

[Lynn Amon]

WG6v2_1.0.zip is not a Bioconductor package.  It is just a zip file with
tables of annotated probe information from Illumina.  You need to use
biocLite to install the Bioconductor packages.  Within R, type:

source("http://bioconductor.org/biocLite.R")
biocLite("lumiHumanv2")

Lynn


Wayne Xu wrote:
> Thanks Ann for the response.
> I use illuminaHumanv2, do you mean it differs from lumiHumanv2?
> I download an annotation file from illumina web site, WG6v2_1.0.zip 
> I could not install it by command: R CMD INSTALL WG6v2_1.0.zip
> Can you give some hints for this installation?
>
> Thanks again,
> Wayne
> --
>
> lumiHumanv2
>
>   
>> Hello Wayne,
>> As the ls() function showed, there is no illuminaHumanv2TARGETID2NUID
>> function in this annotation package.  NUIDs are identifiers invented by
>> the inventors of Lumi.  This package only provides annotation from
>> public databases such as NCBI, KEGG, GO and the like. 
>> Perhaps, you should try the lumiHumanv2 package.
>> Lynn
>>
>>
>> Wayne Xu wrote:
>>   
>>     
>>> Hello,
>>> I got following error when I use illuminaHumanv2 annotation package:
>>>
>>> Error in get(x, envir, mode, inherits) : variable 
>>> "illuminaHumanv2TARGETID2NUID" of mode "environment" was not found
>>>
>>>
>>>  > ls("package:illuminaHumanv2")
>>>  [1] "illuminaHumanv2"             "illuminaHumanv2ACCNUM"
>>>  [3] "illuminaHumanv2CHR"          "illuminaHumanv2CHRLENGTHS"
>>>  [5] "illuminaHumanv2CHRLOC"       "illuminaHumanv2ENTREZID"
>>>  [7] "illuminaHumanv2ENZYME"       "illuminaHumanv2ENZYME2PROBE"
>>>  [9] "illuminaHumanv2GENENAME"     "illuminaHumanv2GO"
>>> [11] "illuminaHumanv2GO2ALLPROBES" "illuminaHumanv2GO2PROBE"
>>> [13] "illuminaHumanv2LOCUSID"      "illuminaHumanv2MAP"
>>> [15] "illuminaHumanv2MAPCOUNTS"    "illuminaHumanv2OMIM"
>>> [17] "illuminaHumanv2ORGANISM"     "illuminaHumanv2PATH"
>>> [19] "illuminaHumanv2PATH2PROBE"   "illuminaHumanv2PFAM"
>>> [21] "illuminaHumanv2PMID"         "illuminaHumanv2PMID2PROBE"
>>> [23] "illuminaHumanv2PROSITE"      "illuminaHumanv2QC"
>>> [25] "illuminaHumanv2QCDATA"       "illuminaHumanv2REFSEQ"
>>> [27] "illuminaHumanv2SUMFUNC"      "illuminaHumanv2SYMBOL"
>>> [29] "illuminaHumanv2UNIGENE"
>>>  > lumi.N.ids <- addNuId2lumi(x1.lumi,lib='illuminaHumanv2')
>>> Error in get(x, envir, mode, inherits) : variable 
>>> "illuminaHumanv2TARGETID2NUID" of mode "environment" was not found
>>>
>>> I tried
>>> file1 <- '12Probeallprofile.txt'
>>>  > x1.lumi<-lumiR(file1, lib='illuminaHumanv2')
>>> I got the same error,
>>>
>>> Thanks in advance
>>>
>>> Wayne
>>> --
>>>
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>>>
>>>       
>
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