Hi, I get "Error in sqliteExecStatement(con, statement, bind.data) : , bind.data must have non-zero dimensions" when run. It seems similar this error https://stat.ethz.ch/pipermail/bioconductor/2011-February/037796.html. I generated the pos file myself. I guess the SEQ_ID on the NDF file is strange but the entry at 194289 and 194290 seems to be OK. SEQ_ID MISMATCH PROBE_CLASS PROBE_ID 194288 CHR9:46353-46389 0 experiment CHR0999P000090528 194289 CHR13:230623-230659 0 experiment CHR1300P000332204 194290 CHR13:595769-595805 0 experiment CHR1300P000337972 194291 CHR1:85497-85533 0 experiment CHR0100P000197636 Any Help would be greatly appreciated... Here is my script library('oligo', quietly=TRUE) library('ff', quietly=TRUE) library('pdInfoBuilder', quietly=TRUE) library('genefilter', quietly=TRUE) library('limma', quietly=TRUE) library('RColorBrewer', quietly=TRUE) palette(brewer.pal(8, "Dark2")) data.dir <- "/microarray-data/ExtractedData/xys" #point to where the data is stored annotation.dir <- "/RNA/NASA/" xys.files <- list.xysfiles(data.dir, full.names = TRUE) pos.file <- list.files(annotation.dir, pattern=".pos", full.names = TRUE) ndf.file <- list.files(annotation.dir, pattern=".ndf", full.names = TRUE) #################################################### ## Make info package MUST have only one POS and ## ## NDF file in the directory ## #################################################### seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf.file, xysFile = xys.files[1], posFile = pos.file, author = "x", email = "x at gmail.com", biocViews = "AnnotationData", genomebuild = "S288C_reference_genome_R49-1-1_20051216", organism = "Yeast", manufacturer="Nimblegen", species = "Saccharomyces cerevisiae", url = "http://google.com") makePdInfoPackage(seed, destDir=annotation.dir) Here is my output: ====================================================================== ========== Building annotation package for Nimblegen Tiling Array NDF: 100507_NYW_BC396_NASA_Yeast_WG.ndf POS: 100507_NYW_BC396_NASA_Yeast_WG.pos XYS: 09_20_Expression_405004_S04.xys ====================================================================== ========== Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.ndf... OK Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.pos... OK Merging NDF and POS files... OK Parsing file: 09_20_Expression_405004_S04.xys... OK Creating package in /home/dougie/Documents/projects/RNA/NASA//pd.100507.nyw.bc396.nasa.yea st.wg Inserting 194289 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 > 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 = annotation.dir) 1: makePdInfoPackage(seed, destDir = annotation.dir) > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] genefilter_1.36.0 Ringo_1.18.0 Matrix_1.0-3 [4] lattice_0.20-0 limma_3.10.2 RColorBrewer_1.0-5 [7] pdInfoBuilder_1.18.0 affxparser_1.26.2 RSQLite_0.11.1 [10] DBI_0.2-5 ff_2.2-5 bit_1.1-8 [13] oligo_1.18.1 oligoClasses_1.16.0 Biobase_2.14.0 [16] stringr_0.6 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.32.1 AnnotationDbi_1.16.16 [4] Biostrings_2.22.0 IRanges_1.12.6 plyr_1.7.1 [7] preprocessCore_1.16.0 splines_2.14.1 survival_2.36-12 [10] xtable_1.7-0 zlibbioc_1.0.0

So we keep a record on the mailing list: the problem was due to the fact that currently pdInfoBuilder expects to find the word "experimental" in the PROBE_CLASS field for the experimental probes. So, replacing "experiment" by "experimental" addressed the issue. benilton On 22 February 2012 06:11, mabawsa <mabawsa at="" gmail.com=""> wrote: > Hi, > I get "Error in sqliteExecStatement(con, statement, bind.data) : , > ?bind.data must have non-zero dimensions" when run. > It seems similar this error > https://stat.ethz.ch/pipermail/bioconductor/2011-February/037796.html. I > generated the pos file myself. > I guess the SEQ_ID on the NDF file is strange but the entry at 194289 and > 194290 seems to be OK. > ? ? ? ? ? ? ? ? ? ?SEQ_ID MISMATCH PROBE_CLASS ? ? ? ? ?PROBE_ID > 194288 ? ?CHR9:46353-46389 ? ? ? ?0 ?experiment CHR0999P000090528 > 194289 CHR13:230623-230659 ? ? ? ?0 ?experiment CHR1300P000332204 > 194290 CHR13:595769-595805 ? ? ? ?0 ?experiment CHR1300P000337972 > 194291 ? ?CHR1:85497-85533 ? ? ? ?0 ?experiment CHR0100P000197636 > > Any Help would be greatly appreciated... > > > Here is my script > > library('oligo', quietly=TRUE) > library('ff', quietly=TRUE) > library('pdInfoBuilder', quietly=TRUE) > library('genefilter', quietly=TRUE) > library('limma', quietly=TRUE) > library('RColorBrewer', quietly=TRUE) > palette(brewer.pal(8, "Dark2")) > > data.dir <- "/microarray-data/ExtractedData/xys" #point to where the data is > stored > annotation.dir <- "/RNA/NASA/" > xys.files <- list.xysfiles(data.dir, full.names = TRUE) > pos.file <- list.files(annotation.dir, pattern=".pos", full.names = TRUE) > ndf.file <- list.files(annotation.dir, pattern=".ndf", full.names = TRUE) > > #################################################### > ## Make info package ?MUST have only one POS and ?## > ## NDF file in the directory ? ? ? ? ? ? ? ? ? ? ?## > #################################################### > seed <- new("NgsTilingPDInfoPkgSeed", > ? ? ? ? ? ?ndfFile = ndf.file, > ? ? ? ? ? ?xysFile = xys.files[1], > ? ? ? ? ? ?posFile = pos.file, > ? ? ? ? ? ?author = "x", > ? ? ? ? ? ?email = "x at gmail.com", > ? ? ? ? ? ?biocViews = "AnnotationData", > ? ? ? ? ? ?genomebuild = "S288C_reference_genome_R49-1-1_20051216", > ? ? ? ? ? ?organism = "Yeast", > ? ? ? ? ? ?manufacturer="Nimblegen", > ? ? ? ? ? ?species = "Saccharomyces cerevisiae", url = "http://google.com") > > makePdInfoPackage(seed, destDir=annotation.dir) > > > Here is my output: > > ==================================================================== ============ > Building annotation package for Nimblegen Tiling Array > NDF: 100507_NYW_BC396_NASA_Yeast_WG.ndf > POS: 100507_NYW_BC396_NASA_Yeast_WG.pos > XYS: 09_20_Expression_405004_S04.xys > ==================================================================== ============ > Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.ndf... OK > Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.pos... OK > Merging NDF and POS files... OK > Parsing file: 09_20_Expression_405004_S04.xys... OK > Creating package in > /home/dougie/Documents/projects/RNA/NASA//pd.100507.nyw.bc396.nasa.y east.wg > Inserting 194289 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 > >> 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 = annotation.dir) > 1: makePdInfoPackage(seed, destDir = annotation.dir) > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 > ?[5] LC_MONETARY=en_GB.UTF-8 ? ?LC_MESSAGES=en_GB.UTF-8 > ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid ? ? ?tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets > [8] methods ? base > > other attached packages: > ?[1] genefilter_1.36.0 ? ?Ringo_1.18.0 ? ? ? ? Matrix_1.0-3 > ?[4] lattice_0.20-0 ? ? ? limma_3.10.2 ? ? ? ? RColorBrewer_1.0-5 > ?[7] pdInfoBuilder_1.18.0 affxparser_1.26.2 ? ?RSQLite_0.11.1 > [10] DBI_0.2-5 ? ? ? ? ? ?ff_2.2-5 ? ? ? ? ? ? bit_1.1-8 > [13] oligo_1.18.1 ? ? ? ? oligoClasses_1.16.0 ?Biobase_2.14.0 > [16] stringr_0.6 > > loaded via a namespace (and not attached): > ?[1] affyio_1.22.0 ? ? ? ? annotate_1.32.1 ? ? ? AnnotationDbi_1.16.16 > ?[4] Biostrings_2.22.0 ? ? IRanges_1.12.6 ? ? ? ?plyr_1.7.1 > ?[7] preprocessCore_1.16.0 splines_2.14.1 ? ? ? ?survival_2.36-12 > [10] xtable_1.7-0 ? ? ? ? ?zlibbioc_1.0.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor