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

[Jack Schonbrun]

Benilton,

Thanks for your suggestions.

By every means I have tested, the file is tab delimited.  And the first row is headers, all other data.

Here is how the first (header) row looks:
PROBE_DESIGN_ID	CONTAINER	DESIGN_NOTE	SELECTION_CRITERIA	SEQ_ID	PROBE_SEQUENCE	MISMATCH	MATCH_INDEX	FEATURE_ID	ROW_NUM	COL_NUM	PROBE_CLASS	PROBE_ID	POSITION	DESIGN_ID	X	Y

Any other details on how the ndf is expected to look?

Thanks again,
Jack





-----Original Message-----
From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] 
Sent: Tuesday, July 14, 2009 1:34 PM
To: Jack Schonbrun
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] makePdInfoPackage in preparation for RMA with oligo on Nimblegen Expression Arrays

Jack,

it looks like your NDF isn't as expected.

When it shows: "inserting 0 rows into table 'featureSet'", it makes me  
wonder how the SEQ_ID column in the NDF looks like.

But, instead of looking at the columns' contents right now, please  
make sure the delimiters of the NDF are tabs. It doesn't appear that's  
the case. Note the warning "In max(ndfdata[["X"]]): no non-missing  
arguments to max; returning -Inf"... It suggests that ndfdata[["X"]]  
is NULL.

Another thing: ensure the first line of the NDF is the header (column  
names) and the data start on the 2nd line.

PLease let me know how it goes.

b

On Jul 14, 2009, at 3:57 PM, Jack Schonbrun wrote:

> 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")
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> ======================================================================
> Building annotation package for Nimblegen Expression Array
> NDF:  test.ndf
> XYS:  test.xys
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> ======================================================================
> 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
>
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