[BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays

[Jack Schonbrun]

Hello,

I would like to use the oligo package to run the RMA algorithm on Nimblegen expression arrays.  To that end, I am attempting to construct an annotation package using makePdInfoPackage().

I have followed the pattern in the "Building Annotation Packages with pdInfoBuilder
for Use with the oligo Package" vignette:

----------------

> ndfFile.test <- "test.ndf"
> xysFile.test <- "test.xys"
> seed.test <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndfFile.test, xysFile = xysFile.test)
> makePdInfoPackage(seed.test, destDir = "./Annotation")
=========================================================================================================================================================================
Building annotation package for Nimblegen Expression Array
NDF:  test.ndf 
XYS:  test.xys 
=========================================================================================================================================================================
Parsing file: test.ndf ... OK
Parsing file: test.xys ... OK
Merging NDF and XYS files ...OK
Preparing contents for featureSet table ...OK
Preparing contents for bgfeature table ...OK
Preparing contents for pmfeature table ...OK
Creating package in ./Annotation/pd.test 
Inserting 0 rows into table "featureSet"... Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (incomplete data binding: expected 2 parameters, got 0)
In addition: Warning messages:
1: In max(ndfdata[["Y"]]) :
  no non-missing arguments to max; returning -Inf
2: In max(ndfdata[["X"]]) :
  no non-missing arguments to max; returning -Inf
3: In sqliteExecStatement(con, statement, bind.data) :
  ignoring zero-row bind.data

------------------

Any help on why it would only be inserting 0 rows, or any of the other messages would be greatly appreciated.  It does make some files in the destDir, but does not run to completion.  Listing of this directory available if it would help.

I am running on Windows XP SP 2.  sessionInfo follows.

> sessionInfo()
R version 2.9.1 (2009-06-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pdInfoBuilder_1.8.1      affxparser_1.16.0        RSQLite_0.7-1            DBI_0.2-4                makePlatformDesign_1.8.0 oligo_1.8.1             
 [7] preprocessCore_1.6.0     oligoClasses_1.6.0       Biobase_2.4.1            affyio_1.12.0           

loaded via a namespace (and not attached):
[1] Biostrings_2.12.7 IRanges_1.2.3     splines_2.9.1     tools_2.9.1    


===========================
Jack Schonbrun Ph.D.
Software Developer
Amyris Biotech