[BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions
Benilton Carvalho
beniltoncarvalho at gmail.com
Mon Aug 26 18:58:57 CEST 2013
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 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
>
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