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;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@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;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@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 Śpd.100929.hg19.deluxe.prom.meth.hx1ą
> >>>
> >>>
> >>> 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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