Can you please give us the results of with(ndf, table(MISMATCH, PROBE_CLASS)) the one thing that pdInfoBuilder expects is the PROBE_CLASS field to have the word 'experimental' for thé probes that are not controls. b On 26 Aug 2013 16:44, "Nitesh Turaga" <nturaga1@jhmi.edu> wrote: > Hi Dr.Carvalho, > > Please let me know your thought process about what exactly you think is > wrong with the "ndf" file. Is it something I'm doing wrong or the ndf file > needs to be re arranged to meet some package requirements? > > Best, > > Nitesh > > On 8/26/13 3:24 PM, "Nitesh Turaga" <nturaga1@jhmi.edu> wrote: > > > > >Hi Dr.Carvalho, > > > > > >> ndf = > >>read.table("100929_HG19_Deluxe_Prom_Meth_HX1.ndf",stringsAsFactors =FALSE, > >> sep='\t', header = TRUE) > >> head(ndf) > > PROBE_DESIGN_ID CONTAINER DESIGN_NOTE > > SELECTION_CRITERIA > >1 537151_1_25 BLOCK1 interval rank > >target_tm:76.00;probe_tm:77.60;freq: 9.25;count:01;rules:0000;score:0812 > >2 537151_1_27 BLOCK1 interval rank > >target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;score :0828 > >3 537151_1_29 BLOCK1 interval rank > >target_tm:76.00;probe_tm:86.60;freq: 3.31;count:01;rules:0000;score:0706 > >4 537151_1_31 BLOCK1 interval rank > >target_tm:76.00;probe_tm:75.70;freq:14.11;count:01;rules:0000;score :0808 > >5 537151_1_33 BLOCK1 interval rank > >target_tm:76.00;probe_tm:83.30;freq: 6.92;count:01;rules:0000;score:0719 > >6 537151_1_35 BLOCK1 interval rank > >target_tm:76.00;probe_tm:77.60;freq:10.97;count:01;rules:-400;score :0400 > > SEQ_ID > >PROBE_SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM > >1 chr19:6588109-6599163 > >AAAAGACCAGAAAACAGGGCACGGACGTAAGCAGAGAGGTTCTATGTGTC 0 254819035 > >254819035 25 > >2 chr5:83677266-83688611 > >GGAGTTACATATCCTTATCAAATCCCAGGCATTAATGCAAGTAAATTGCAACCCATACG 0 > >254968001 254968001 27 > >3 chr11:1302527-1303227 > >GTGCACACAGGCCCGAAGCCACGCAGCCAGCACCGCGTAGCCAGGCAGAG 0 254918787 > >254918787 29 > >4 chr19:22015970-22026977 > >GAGGCAGATTTGCCTGACATAGTTCTCAACTTGACTTTTCTAGTGGCTTAGTAATTTTG 0 > >254575363 254575363 31 > >5 chrX:37200527-37211589 > >GACCGCGAGGCTTGCCAACGGTGCTGGAGGGTGTCCCAGCTTCAAGTTCA 0 254695458 > >254695458 33 > >6 chr14:24592674-24644677 > >CAAACTGGATTCCTTGCTCTATCTAAGCCCCATAAAAGACACTCTGGCCG 0 254313287 > >254313287 35 > > COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y DMD > >1 1 CHR19FS006590155 6590155 537151 1 25 A03 > >2 1 CHR05FS083677686 83677686 537151 1 27 A03 > >3 1 CHR11FS001302927 1302927 537151 1 29 A03 > >4 1 CHR19FS022021016 22021016 537151 1 31 A03 > >5 1 CHRXFS037208928 37208928 537151 1 33 A03 > >6 1 CHR14FS024636274 24636274 537151 1 35 A03 > > > > > >> with(ndf,table(MISMATCH)) > >MISMATCH > > 0 > >2186885 > > > > > >Best, > > > >Nitesh > >________________________________________ > >From: Benilton Carvalho [beniltoncarvalho@gmail.com] > >Sent: Monday, August 26, 2013 3:17 PM > >To: Nitesh Turaga > >Subject: Re: Reg: makePdInfoPackage Error in sqliteExecStatement(con, > >statement, bind.data) : bind.data must have non-zero dimensions > > > >Hi Nitesh, > > > > > >can you please "re-read" the ndf? use: > > > >ndf = read.table("100929_HG19_Deluxe_Prom_Meth_HX1.ndf", > >stringsAsFactors=FALSE, sep='\t', header=TRUE) > > > >then, try the other command I sent you: > > > >with(ndf, table(MISMATCH)) > > > >also, please copy back the mailing list, so others can also help. > > > >b > > > >2013/8/26 Nitesh Turaga <nturaga1@jhmi.edu>: > >> Hi Dr.Carvalho, > >> > >> This is the result I am getting. I'm not sure what MISMATCH is in this > >>case. So it is not evaluating that function. > >> > >> Nitesh > >> > >>> ndf = read.table("100929_HG19_Deluxe_Prom_Meth_HX1.ndf", > >>>stringsAsFactors=FALSE, sep='\t') > >>> head(ndf) > >> V1 V2 V3 > >> 1 PROBE_DESIGN_ID CONTAINER DESIGN_NOTE > >> 2 537151_1_25 BLOCK1 interval rank > >> 3 537151_1_27 BLOCK1 interval rank > >> 4 537151_1_29 BLOCK1 interval rank > >> 5 537151_1_31 BLOCK1 interval rank > >> 6 537151_1_33 BLOCK1 interval rank > >> > >>V4 V5 > >> 1 > >>SELECTION_CRITERIA SEQ_ID > >> 2 target_tm:76.00;probe_tm:77.60;freq: > >>9.25;count:01;rules:0000;score:0812 chr19:6588109-6599163 > >> 3 > >>target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;scor e:0828 > >>chr5:83677266-83688611 > >> 4 target_tm:76.00;probe_tm:86.60;freq: > >>3.31;count:01;rules:0000;score:0706 chr11:1302527-1303227 > >> 5 > >>target_tm:76.00;probe_tm:75.70;freq:14.11;count:01;rules:0000;scor e:0808 > >>chr19:22015970-22026977 > >> 6 target_tm:76.00;probe_tm:83.30;freq: > >>6.92;count:01;rules:0000;score:0719 chrX:37200527-37211589 > >> V6 V7 > >> V8 V9 V10 > >> 1 PROBE_SEQUENCE MISMATCH > >>MATCH_INDEX FEATURE_ID ROW_NUM > >> 2 AAAAGACCAGAAAACAGGGCACGGACGTAAGCAGAGAGGTTCTATGTGTC 0 > >>254819035 254819035 25 > >> 3 GGAGTTACATATCCTTATCAAATCCCAGGCATTAATGCAAGTAAATTGCAACCCATACG 0 > >>254968001 254968001 27 > >> 4 GTGCACACAGGCCCGAAGCCACGCAGCCAGCACCGCGTAGCCAGGCAGAG 0 > >>254918787 254918787 29 > >> 5 GAGGCAGATTTGCCTGACATAGTTCTCAACTTGACTTTTCTAGTGGCTTAGTAATTTTG 0 > >>254575363 254575363 31 > >> 6 GACCGCGAGGCTTGCCAACGGTGCTGGAGGGTGTCCCAGCTTCAAGTTCA 0 > >>254695458 254695458 33 > >> V11 V12 V13 V14 V15 V16 V17 V18 > >> 1 COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y DMD > >> 2 1 CHR19FS006590155 6590155 537151 1 25 A03 > >> 3 1 CHR05FS083677686 83677686 537151 1 27 A03 > >> 4 1 CHR11FS001302927 1302927 537151 1 29 A03 > >> 5 1 CHR19FS022021016 22021016 537151 1 31 A03 > >> 6 1 CHRXFS037208928 37208928 537151 1 33 A03 > >> > >> > >> > >> ________________________________________ > >> From: Benilton Carvalho [beniltoncarvalho@gmail.com] > >> Sent: Monday, August 26, 2013 12:58 PM > >> To: Nitesh Turaga > >> Cc: bioconductor@r-project.org; mabawsa@gmail.com > >> Subject: Re: Reg: makePdInfoPackage Error in sqliteExecStatement(con, > >>statement, bind.data) : bind.data must have non-zero dimensions > >> > >> 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@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;sco re: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@andrew.cmu.edu <mailto:nturaga1@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 Œpd.100929.hg19.deluxe.prom.meth.hx1¹ > >>> > >>> > >>> 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 > >>> > > > > [[alternative HTML version deleted]]

Hi, Quick question, to which column in the ndf file does "bgfeature" correspond to? And how should the values look like? After replacing the empty string with experimental, I'm getting this error now. > 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: 15433N_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: 15433N_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 [[alternative HTML version deleted]]