[BioC] Error using pdInfoBuilder v1.14.1 for NimbleGen Array

Kate Turner kturner at oriongenomics.com
Fri Feb 11 17:45:20 CET 2011 

Hello,

After my update, I still find I get the same 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//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

My session Info is:

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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_1.14.1 oligo_1.14.0         oligoClasses_1.12.2
affxparser_1.22.1  
[5] RSQLite_0.9-4        DBI_0.2-5            Biostrings_2.18.2
IRanges_1.8.8      
[9] Biobase_2.10.0 

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0 splines_2.12.1
tools_2.12.1  

And traceback gives:

> traceback()
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/")

Has anyone encountered this error previously?

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.

Many Thanks,

Kate


On 2/10/11 2:12 PM, "Vincent Carey" <stvjc at channing.harvard.edu> wrote:

> 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
>> 
>> 
>>        [[alternative HTML version deleted]]
>> 
>> 
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