To avoid this error:


Parsing file: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.ndf... OK
Parsing file: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.pos... OK
Merging NDF and POS files... OK
Parsing file: 15433N+AF8-532.xys... OK
Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1
Inserting 30291 rows into table featureSet... OK
Inserting 2161586 rows into table pmfeature... OK
Inserting 0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) :
  bind.data must have non-zero dimensions


1. Make sure you the probes which are labeled +ACI-experimental+ACI- are not the ones with no sequences in the +ACI-PROBE+AF8-SEQUENCE+ACI-.

2.  In the CONTAINER column of the ndf file, if you read in the ndf+AF8-file and look at the table, +ACI- table(ndf+AF8-file+ACQ-CONTAINER)+ACI-, this should show you that a specific class of probes which have the maximum number (it will be much larger than any of the other CONTAINER classes). Label only this with the probe class as +ACI-experimental+ACI-.

In the case of 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.ndf, label only probes with +ACI-BLOCK 1+ACI- in the CONTAINER column, with +ACI-experimental+ACI- in the PROBE+AF8-CLASS.

This code should do the above suggested,

ndf+AF8-file +AD0- read.table(+ACI-100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.ndf+ACI-,sep +AD0- +ACIAXA-t+ACI-,stringsAsFactor +AD0-F,header +AD0-T)
ndf+ACQ-PROBE+AF8-CLASS+AFs-ndf+ACQ-CONTAINER +AD0APQ- +ACI-BLOCK1+ACIAXQ- +AD0- +ACI-experimental+ACI-

Please make sure you don't write to the original file. Use a different filename.

write.table(+ACI-100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1+AF8-edited.ndf+ACI-,sep +AD0- +ACIAXA-t+ACI-,quote +AD0-F)

Best,

Nitesh


+AF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBf-

Hi,

Quick question, to which column in the ndf file does +ACI-bgfeature+ACI- correspond to? And how should the values look like?

After replacing the empty string with experimental, I'm getting this error now.

+AD4- makePdInfoPackage(pkg,destDir +AD0- +ACI-.+ACI-)
+AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQ-
Building annotation package for Nimblegen Tiling Array
NDF: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.ndf
POS: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.pos
XYS: 15433N+AF8-532.xys
+AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQ-
Parsing file: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.ndf... OK
Parsing file: 100929+AF8-HG19+AF8-Deluxe+AF8-Prom+AF8-Meth+AF8-HX1.pos... OK
Merging NDF and POS files... OK
Parsing file: 15433N+AF8-532.xys... OK
Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1
Inserting 30291 rows into table featureSet... OK
Inserting 2161586 rows into table pmfeature... OK
Inserting 0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) :
  bind.data must have non-zero dimensions


Best,

Nitesh

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