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Nitesh Turaga
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@nitesh-turaga-6112
Last seen 10.3 years ago
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:08
28
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:08
08
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:04
00
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 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:0
828
>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:0
808
>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 ?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
>>
