[BioC] Error using pdInfoBuilder for NimbleGen Array

[Vincent Carey]

You will probably get better assistance if you upgrade R to 2.12.1 and
then update your pdInfoBuilder which is now at 1.14.1 for release.

On Thu, Feb 10, 2011 at 2:56 PM, Kate Turner <kturner at oriongenomics.com> wrote:
>
> Hello,
>
> I am trying to build an info package for a NimbleGen Tiling array. The
> experiment is a dye swap, so I have a pair of xys files for each sample. The
> array is custom built.
>
> I have:
> 1.  xys files generated from pair files by Nimblescan.
> 2. An ndf file
> 3. A pos file.
>
> The pos file wasn't generated by NimbleGen. I had to generate it myself and
> used a pos file I found on line as an example. I saved my file as a tab
> delimited txt and changed the .txt to .pos in Aquamacs.
>
>
> When I try and generate the annotation package I get the following error
> message:
>
>
> Building annotation package for Nimblegen Tiling Array
> NDF: 101219_HG_Orion_SS_CGH.ndf
> POS: NDF_OGHA.pos
> XYS: 467246_Slot2_Cycle1_Orion_2011-02-07_532.xys
> ============================================================================
> =============================
> Parsing file: 101219_HG_Orion_SS_CGH.ndf... OK
> Parsing file: NDF_OGHA.pos... OK
> Merging NDF and POS files... OK
> Parsing file: 467246_Slot2_Cycle1_Orion_2011-02-07_532.xys... OK
> Creating package in
> /Users/kturner/Desktop/Project_I//pd.101219.hg.orion.ss.cgh
> Inserting 2 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
>
> The above error message suggests that the program is having issues creating
> the featureSet, pmfeature and bgfeature. I have generated an annotation
> package for a custom built expression array and that was successful.  In the
> case of the expression annotation package there were >1000 rows in all
> tables associated with the build.
>
> In the output associated with the expression array annotation package, the
> ndf and the xys files were merged. I am wondering if the xys file for the
> tiling array should also be merged to the tiling array ndf and pos files?
>
> The global structure of my ndf and xys files for the tiling array are
> similar to those for the expression array. Additionally the structure of the
> xys looks similar to that in the post by Alex Rodriquez in Feb. 2010, so I
> am assuming (perhaps incorrectly) that it isn't the xys or the ndf that are
> the issue, but the pos file.
>
> In my pos file, I have each feature represented, even if it is duplicated. I
> also have  features that do not have a known chromosome position, and these
> features have a blank for some of their variables in the file.  I have been
> told that NimbleGen pos files donšt have to have the same number of features
> found on the array itself.
>
> Does anyone know if pdInfoBuilder expects a particular structure for a .pos
> file. For instance, does there need to be 1 row for each feature on the
> array irrespective of duplication and do blanks need to be annotated with
> N/A for instance.
>
>
> I am new to building  annotation packages and wondered if someone with more
> experience could help?
>
>
> My session info is:
>
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pdInfoBuilder_1.12.0 oligo_1.12.2         oligoClasses_1.10.0
> affxparser_1.20.0
> [5] RSQLite_0.9-2        DBI_0.2-5            Biostrings_2.16.9
> IRanges_1.6.17
> [9] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 splines_2.11.1
>
>
> and output of traceback is:
>
> 8: stop("bind.data must have non-zero dimensions")
> 7: sqliteExecStatement(con, statement, bind.data)
> 6: sqliteQuickSQL(conn, statement, bind.data, ...)
> 5: dbGetPreparedQuery(conn, sql_template, bind.data = data)
> 4: dbGetPreparedQuery(conn, sql_template, bind.data = data)
> 3: dbInsertDataFrame(conn, "pmfeature", parsedData[["pmFeatures"]],
>       tiledRegionPmFeatureSchema[["col2type"]], !quiet)
> 2: makePdInfoPackage(seed, destDir = "/Users/kturner/Desktop/")
> 1: makePdInfoPackage(seed, destDir = "/Users/kturner/Desktop/")
>
> Many thanks in advance for any help,
>
> Kate
>
> Orion Genomics
>
>
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>
>
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