Hi and thank you for your answer Dr. Carvalho,

I read the NDF manually. There are numbers from 1 to 461 in the PROBE_CLASS
column.

Is the solution to change the numbers into word "experimental"?

Thank you,

Zeynep

2012/4/24 Benilton Carvalho <beniltoncarvalho@gmail.com>

> If you read the NDF manually, what are the values for the column
> PROBE_CLASS? The builder expects to find the value "experimental"... And
> yours does not seem to be the case.
>
>
> On Tuesday, 24 April 2012, zeynep özkeserli wrote:
>
>> Hi all,
>>
>> I am trying to analyze Nimblegen Human 2.1 M Deluxe Promoter array data
>> using Charm package. My problem is, when I try to import the xys data,
>> program needs the platform design file, as usual, tries to download from
>> BioConductor website but prompts out this error and stops.
>>
>> ...
>> Loading required package: pd.100929.hg19.deluxe.prom.meth.hx1
>> Attempting to obtain 'pd.100929.hg19.deluxe.prom.meth.hx1' from
>> BioConductor website.
>> Checking to see if your internet connection works...
>> Package 'pd.100929.hg19.deluxe.prom.meth.hx1' was not found in the
>> BioConductor repository.
>> The 'pdInfoBuilder' package can often be used in situations like this.
>> ...
>>
>>
>> So I tried the pdInfoBuilder package to solve my problem. But it also
>> didn't work. Here is what I do and the errors I get:
>>
>> I took the code from this address and modified for myself:
>>
>> http://www.biostat.jhsph.edu/~maryee/charm/index.php/Main/MakingANewArrayAnnotationPackage
>>
>>
>>
>> library(pdInfoBuilder)
>> ndf <- list.files(pattern = ".ndf", full.names = TRUE)
>> pos <- list.files(pattern = ".pos", full.names = TRUE)
>> xys <- list.files(pattern = ".xys", full.names = TRUE)[1]
>> seed <- new("NgsTilingPDInfoPkgSeed",
>>    ndfFile = ndf, xysFile = xys,
>>    posFile = pos,
>>    author = "Martin Aryee",
>>    version = "0.99.0",
>>    email = "myemail@jhu.edu",
>>    biocViews = "AnnotationData",
>>    genomebuild = "HG 18", organism = "Human",
>>    species = "Homo sapiens")
>> makePdInfoPackage(seed, destDir = ".")
>>
>>
>> *After the code worked for 2 hours, I got these errors:*
>>
>>
>>
>> Building annotation package for Nimblegen Tiling Array
>> NDF: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf
>>
>> POS: 100929_HG19_Deluxe_Prom_Meth_HX1.pos
>> XYS: 503534_532.xys
>>
>> ==================================================================================
>> Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf... OK
>> Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.pos... OK
>> Merging NDF and POS files... OK
>> Parsing file: 503534_532.xys... OK
>> Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1
>> Inserting 30291 rows into table featureSet... OK
>> Inserting 0 rows into table pmfeature... Error in
>> sqliteExecStatement(con, statement, bind.data) :
>>  bind.data must have non-zero dimensions
>>
>>
>> I really can't figure out what the problem is. Can anybody offer any
>> solutions?
>>
>> Thank you in advance! :)
>>
>> Zeynep Ozkeserli
>> Ankara University Biotechnology Institute
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>

	[[alternative HTML version deleted]]

