Entering edit mode
Jack Schonbrun
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50
@jack-schonbrun-3572
Last seen 9.6 years ago
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