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 +AF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AX wBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8 AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfA F8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwB fAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AX wBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8 AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfA F8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwB fAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBfAF8AXwBf- 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-) +AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0AP QA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0 APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9A D0APQ- 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 +AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0AP QA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0 APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9AD0APQA9A D0APQ- 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 +AFsAWw-alternative HTML version deleted+AF0AXQ- [[alternative HTML version deleted]]