
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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