[BioC] illumina annotation package error

[Wayne Xu]

Thanks Lynn,
It works now. They are two different packages,

Wayne
--

Lynn Amon wrote:
> 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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