Question: Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
0
gravatar for Nitesh Turaga
6.1 years ago by
Nitesh Turaga50 wrote:
Hi, I'm a little stuck with the charm analysis using MeDip arrays. It started with an error at "readCharm" and trickled into the finer details of what information the function needed. I have seen the previous question in https://stat.ethz.ch/pipermail/bioconductor/2012-February/043719.html . Here, the user built a custom ".pos" file. But the ".pos" file i'm using is from nimblegen and so is the ".ndf". I do not have a column in which "experimental" or otherwise is mentioned. My .pos file looks like this, PROBE_ID SEQ_ID CHROMOSOME POSITION COUNT LENGTH GC CHR01FS000015738 chr1:15366-44081 chr1 15738 3 50 0.68 CHR01FS000016058 chr1:15366-44081 chr1 16058 2 50 0.70 CHR01FS000016770 chr1:15366-44081 chr1 16770 5 50 0.54 And my .ndf file looks like this. PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUE NCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID PO SITION DESIGN_ID X Y DMD 537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: 9.25;count:01;rules:0000;score:0812 chr19:6588109-6599163 AAAAGACCAGAAAACAG GGCACGGACGTAAGCAGAGAGGTTCTATGTGTC 0 254819035 254819035 25 1 CHR19FS006590 155 6590155 537151 1 25 A03 537151_1_27 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;score:08 28 chr5:83677266-83688611 GGAGTTACATATCCTTATCAAATCCCAGGCATTAATGCAAGTAAATTGC AACCCATACG 0 254968001 254968001 27 1 CHR05FS083677686 83677686 537151 1 2 7 A03 > ndf = list.files(".",pattern = ".ndf",full.names = TRUE) > pos = list.files(".",pattern = ".pos",full.names = TRUE)[1] > files = list.files("Lung Cancer/2.1M/XYS",pattern = ".xys",full.names = >T)[1] > pkg = new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = >files,posFile = pos, author = "Nitesh Turaga",email = >"nturaga at andrew.cmu.edu <mailto:nturaga1 at="" jhmi.edu="">",biocViews = >"DNAMethylation",genomebuild = "NCBI Build 36",organism = "Human",species >= "Homo Sapiens") > makePdInfoPackage(pkg,destDir=".") ====================================================================== ===== ===== Building annotation package for Nimblegen Tiling Array NDF: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf POS: 100929_HG19_Deluxe_Prom_Meth_HX1.pos XYS: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys ====================================================================== ===== ===== Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf... OK Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.pos... OK Merging NDF and POS files... OK Parsing file: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys... OK Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1 Inserting 30291 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 = ".") 1: makePdInfoPackage(seed, destDir = ".") > sessionInfo() R version 2.15.2 Patched (2013-02-08 r61876) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] RColorBrewer_1.0-5 limma_3.14.4 genefilter_1.40.0 [4] pdInfoBuilder_1.22.0 affxparser_1.30.2 RSQLite_0.11.2 [7] DBI_0.2-5 ff_2.2-10 bit_1.1-9 [10] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 [13] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.3 [4] BiocInstaller_1.8.3 Biostrings_2.26.3 codetools_0.2-8 [7] foreach_1.4.0 GenomicRanges_1.10.6 IRanges_1.16.4 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 survival_2.37-2 [16] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 NOTE: I am doing the above process because this was the error I encountered before. This is the specific error I was getting and there was no package called pd.100929.hg19.deluxe.prom.meth.hx1. >files = list.files("XYS/") > fileNames = list.files("XYS/") > rawData = readCharm(files = fileNames, path ="XYS/",ut = "_532.xys",md = >"_635.xys") Loading required package: pd.100929.hg19.deluxe.prom.meth.hx1 Attempting to obtain 'pd.100929.hg19.deluxe.prom.meth.hx1' from BioConductor website. Checking to see if your internet connection works... Package 'pd.100929.hg19.deluxe.prom.meth.hx1' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in read.xysfiles2(channel1 = file.path(path, files2Ut), channel2 = file.path(path, : Must install the pd.100929.hg19.deluxe.prom.meth.hx1 package. In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ?pd.100929.hg19.deluxe.prom.meth.hx1? I read the pdInfoBuilder package reference, charm reference. I am not able to find a reply to solve this problem. I could use the help. Thank you, Best, Nitesh -- Nitesh Turaga MS in Computational Biology Carnegie Mellon University -- Nitesh Turaga MS in Computational Biology Carnegie Mellon University
ADD COMMENTlink modified 6.1 years ago by Benilton Carvalho4.3k • written 6.1 years ago by Nitesh Turaga50
Answer: Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) :
0
gravatar for Benilton Carvalho
6.1 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
If you read the NDF with ndf = read.table('name_of_ndf', stringsAsFactors=FALSE, sep='\t') what do you get for head(ndf) with(ndf, table(MISMATCH)) ? At this point, what worries me is the message: "Inserting 0 rows into table pmfeature" which says that the software is unable to identify the PM probes from your design. b 2013/8/26 Nitesh Turaga <nturaga1 at="" jhmi.edu="">: > Hi, > > I'm a little stuck with the charm analysis using MeDip arrays. It started > with an error at "readCharm" and trickled into the finer details of what > information the function needed. > > I have seen the previous question in > https://stat.ethz.ch/pipermail/bioconductor/2012-February/043719.html . > Here, the user built a custom ".pos" file. But the ".pos" file i'm using > is from nimblegen and so is the ".ndf". I do not have a column in which > "experimental" or otherwise is mentioned. > > My .pos file looks like this, > > PROBE_ID SEQ_ID CHROMOSOME POSITION COUNT LENGTH GC > CHR01FS000015738 chr1:15366-44081 chr1 15738 3 50 0.68 > CHR01FS000016058 chr1:15366-44081 chr1 16058 2 50 0.70 > CHR01FS000016770 chr1:15366-44081 chr1 16770 5 50 0.54 > > And my .ndf file looks like this. > PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID PROBE_SEQUE > NCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID PO > SITION DESIGN_ID X Y DMD > 537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: > 9.25;count:01;rules:0000;score:0812 chr19:6588109-6599163 AAAAGACCAGAAAACAG > GGCACGGACGTAAGCAGAGAGGTTCTATGTGTC 0 254819035 254819035 25 1 CHR19FS006590 > 155 6590155 537151 1 25 A03 > 537151_1_27 BLOCK1 interval > rank target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;score:08 > 28 chr5:83677266-83688611 GGAGTTACATATCCTTATCAAATCCCAGGCATTAATGCAAGTAAATTGC > AACCCATACG 0 254968001 254968001 27 1 CHR05FS083677686 83677686 537151 1 2 > 7 A03 > > > > >> ndf = list.files(".",pattern = ".ndf",full.names = TRUE) > >> pos = list.files(".",pattern = ".pos",full.names = TRUE)[1] >> files = list.files("Lung Cancer/2.1M/XYS",pattern = ".xys",full.names = >>T)[1] >> pkg = new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = >>files,posFile = pos, author = "Nitesh Turaga",email = >>"nturaga at andrew.cmu.edu <mailto:nturaga1 at="" jhmi.edu="">",biocViews = >>"DNAMethylation",genomebuild = "NCBI Build 36",organism = "Human",species >>= "Homo Sapiens") >> makePdInfoPackage(pkg,destDir=".") > ==================================================================== ======= > ===== > Building annotation package for Nimblegen Tiling Array > NDF: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf > POS: 100929_HG19_Deluxe_Prom_Meth_HX1.pos > XYS: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys > ==================================================================== ======= > ===== > > Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf... OK > Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.pos... OK > Merging NDF and POS files... OK > Parsing file: 542585A01_Sample12_2013-06-27_12-16_2013-07_532.xys... OK > Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1 > > Inserting 30291 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 = ".") > 1: makePdInfoPackage(seed, destDir = ".") >> sessionInfo() > R version 2.15.2 Patched (2013-02-08 r61876) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] RColorBrewer_1.0-5 limma_3.14.4 genefilter_1.40.0 > [4] pdInfoBuilder_1.22.0 affxparser_1.30.2 RSQLite_0.11.2 > [7] DBI_0.2-5 ff_2.2-10 bit_1.1-9 > [10] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 > > [13] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.3 > [4] BiocInstaller_1.8.3 Biostrings_2.26.3 codetools_0.2-8 > [7] foreach_1.4.0 GenomicRanges_1.10.6 IRanges_1.16.4 > [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 > [13] splines_2.15.2 stats4_2.15.2 survival_2.37-2 > [16] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > > > > > NOTE: > > I am doing the above process because this was the error I encountered > before. This is the specific error I was getting and there was no package > called pd.100929.hg19.deluxe.prom.meth.hx1. > >>files = list.files("XYS/") >> fileNames = list.files("XYS/") >> rawData = readCharm(files = fileNames, path ="XYS/",ut = "_532.xys",md = >>"_635.xys") > Loading required package: pd.100929.hg19.deluxe.prom.meth.hx1 > Attempting to obtain 'pd.100929.hg19.deluxe.prom.meth.hx1' from > BioConductor website. > Checking to see if your internet connection works... > Package 'pd.100929.hg19.deluxe.prom.meth.hx1' was not found in the > BioConductor repository. > The 'pdInfoBuilder' package can often be used in situations like this. > Error in read.xysfiles2(channel1 = file.path(path, files2Ut), channel2 = > file.path(path, : > Must install the pd.100929.hg19.deluxe.prom.meth.hx1 package. > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called ?pd.100929.hg19.deluxe.prom.meth.hx1? > > > I read the pdInfoBuilder package reference, charm reference. I am not able > to find a reply to solve this problem. > > I could use the help. > > > Thank you, > > Best, > > Nitesh > > > > > -- > > > Nitesh Turaga > MS in Computational Biology > Carnegie Mellon University > > > > > > -- > > > Nitesh Turaga > MS in Computational Biology > Carnegie Mellon University >
ADD COMMENTlink written 6.1 years ago by Benilton Carvalho4.3k
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