[BioC] Reg: makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions

Nitesh Turaga nturaga1 at jhmi.edu
Mon Aug 26 21:24:19 CEST 2013


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 at 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 at 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;score: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;score: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 at gmail.com]
> Sent: Monday, August 26, 2013 12:58 PM
> To: Nitesh Turaga
> Cc: bioconductor at r-project.org; mabawsa at 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 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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