[BioC] Oligo:read.xysfiles fails
Arvas Mikko
Mikko.Arvas at vtt.fi
Tue Nov 11 10:57:27 CET 2008
Hi Benilton,
Thank you very much for a fast reply!
I tried your command and I can get it to work if I have a 'pos' i.e. for
CGH etc. tiling arrays, but for conventional expression I don't have a
'pos' file and thus it does not work in my hands, see details below.
Given that I have for CGH 2M probes the speed of data handling is very
good, thank you very much for that!
For expression arrays, can I somehow circumvent the 'pos' file
requirement or do I have to somehow create a 'pos' file?
Here is my unsuccesful trial w/o pos file:
> objE <- new("NgsExpressionPDInfoPkgSeed",
version="0.0.1",
author="Mikko Arvas", email="mikko.arvas at vtt.fi",
biocViews="AnnotationData",
genomebuild="Trichoderma reesei version 2",
ndfFile="TR_AM_TilingStripped.ndf",posFile=NA,xysFile="B_32h_31.xys")
> makePdInfoPackage(objE, destDir=".")
Creating package in ./pd.tr.am.tilingstripped
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (incomplete data binding: expected 2 parameters, got 0)
In addition: Warning messages:
1: In max(i) : no non-missing arguments to max; returning -Inf
2: In sqliteExecStatement(con, statement, bind.data) :
ignoring zero-row bind.data
Timing stopped at: 0.116 0 0.116
Here is the succesful trial w/ pos file:
> objT <- new("NgsTilingPDInfoPkgSeed",
version="0.0.1",
author="Mikko Arvas", email="mikko.arvas at vtt.fi",
biocViews="AnnotationData",
genomebuild="Trichoderma reesei version 2",
ndfFile="2007-05-02_TriRee2_MV_CGH_HX1.ndf",posFile="2007-05-02_TriRee2_
MV_CGH_HX1.O.pos",xysFile="17786902_532.pair.xys")
> makePdInfoPackage(objT, destDir=".")
Creating package in ./pd.2007.05.02.triree2.mv.cgh.hx1
loadUnitsByBatch took 112.83 sec
loadAffySeqCsv took 621.23 sec
DB sort, index creation took 1212.18 sec
[1] TRUE
Warning message:
In max(i) : no non-missing arguments to max; returning -Inf
# R CMD INSTALL pd.2007.05.02.triree2.mv.cgh.hx1/
* Installing to library '/usr/local/lib64/R-2.8.0/lib64/R/library'
* Installing *source* package 'pd.2007.05.02.triree2.mv.cgh.hx1' ...
** R
** inst
** preparing package for lazy loading
Loading required package: RSQLite
Loading required package: DBI
Loading required package: oligoClasses
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
No man pages found in package 'pd.2007.05.02.triree2.mv.cgh.hx1'
** building package indices ...
* DONE (pd.2007.05.02.triree2.mv.cgh.hx1)
> test1 <-
read.xysfiles(list.xysfiles(),pkg="pd.2007.05.02.triree2.mv.cgh.hx1")
> test1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2173626 features, 2 samples
element names: exprs
phenoData
sampleNames: 1, 2
varLabels and varMetadata description: none
featureData
featureNames: 1, 2, ..., 2173626 (2173626 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: pd.2007.05.02.triree2.mv.cgh.hx1
> head(exprs(test1))
1 2
1 21787.33 15644.44
2 7246.67 5632.78
3 10693.89 8699.67
4 2110.78 1882.56
5 17676.00 15148.56
6 15915.33 13322.89
-----Original Message-----
From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
Sent: 10. marraskuuta 2008 23:10
To: Arvas Mikko
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: Oligo:read.xysfiles fails
Hello Mikko,
we are in the process of migrating the annotation packages used by oligo
to a more efficient structure that uses SQL, saving you more RAM for
analysis. That said, you'll build your annotation package using the
pdInfoBuilder package.
For example:
library(pdInfoBuilder)
ndfFile <- "theNDF.ndf"
posFile <- "thePOS.pos"
xysFile <- "theXYS.xys"
obj <- new("NgsTilingPDInfoPkgSeed",
version="0.0.1",
author="Benilton Carvalho", email="bcarvalh at jhsph.edu",
biocViews="AnnotationData",
genomebuild="NCBI Build 36",
ndfFile=ndfFile,
posFile=posFile,
xysFile=xysFile)
makePdInfoPackage(obj, destDir=".")
please let us know how it goes,
b
On Nov 10, 2008, at 11:43 AM, Arvas Mikko wrote:
> Hi,
>
> I am trying to use makePDpackage and oligo to process Nimblegen
> arrays, but I get an error in read.xysfiles:
> > test.exprs <- read.xysfiles(list.xysfiles(),pkg='pd.tr.am.tiling')
> Loading required package: pd.tr.am.tiling Error in
> geometry(get(pkgname)) :
> no slot of name "geometry" for this object of class "platformDesign"
>
> This error does not happen in R 2.5.1 with oligo 1.0.2-6 I notice that
> other users have had the same error message:
> http://article.gmane.org/gmane.science.biology.informatics.conductor/1
> 9508/
> https://stat.ethz.ch/pipermail/bioc-devel/attachments/20080715/df48e1a
> d/attachment.pl
> http://article.gmane.org/gmane.science.biology.informatics.conductor/1
> 9251/
>
> Unfortunately, they have not received help on this issue, but maybe
> somebody could still help me?
>
> All the best,
> Mikko Arvas
>
>
>
> Here is the whole set of commands:
>
> First I make the PD package:
> > library(makePlatformDesign)
> >
> makePDpackage
> ("TR_AM_Tiling
> .ndf","13347602_532_pair.txt.xys",manufacturer='nimblegen')
> nimblegen expression
> The package will be called pd.tr.am.tiling Reading TR_AM_Tiling.ndf
> Assuming a simple design (NOT multiple-wells).
> Creating package in /pd.tr.am.tiling
> [1] "pd.tr.am.tiling"
>
> Then I install it:
> # R CMD INSTALL pd.tr.am.tiling/
> * Installing to library '/usr/local/lib64/R-2.8.0/lib64/R/library'
> * Installing *source* package 'pd.tr.am.tiling' ...
> ** R
> ** data
> ** preparing package for lazy loading
> ** help
> chmod: cannot access `/usr/local/lib64/R-2.8.0/lib64/R/library/
> pd.tr.am.tiling/man/pd.tr.am.tiling.Rd.gz': No such file or directory
>
> >>> Building/Updating help pages for package 'pd.tr.am.tiling'
> Formats: text html latex example
> ** building package indices ...
> Warning in max.default(numeric(0), na.rm = FALSE) :
> no non-missing arguments to max; returning -Inf
> * DONE (pd.tr.am.tiling)
>
> And try to read in xys files:
> > test.exprs <- read.xysfiles(list.xysfiles(),pkg='pd.tr.am.tiling')
> Loading required package: pd.tr.am.tiling Error in
> geometry(get(pkgname)) :
> no slot of name "geometry" for this object of class "platformDesign"
>
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE
> =
> en_US
> .UTF
> -8
> ;LC_NUMERIC
> =
> C
> ;LC_TIME
> =
> en_US
> .UTF
> -8
> ;LC_COLLATE
> =
> en_US
> .UTF
> -8
> ;LC_MONETARY
> =
> C
> ;LC_MESSAGES
> =
> en_US
> .UTF
> -8
> ;LC_PAPER
> =
> en_US
> .UTF
> -8
> ;LC_NAME
> =
> C
> ;LC_ADDRESS
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils
> datasets
> [8] methods base
>
> other attached packages:
> [1] limma_2.16.2 pd.tr.am.tilingori_1.6.0
> makePlatformDesign_1.6.0
> [4] oligo_1.6.0 oligoClasses_1.4.0
> affxparser_1.14.0
> [7] AnnotationDbi_1.4.0 preprocessCore_1.4.0 RSQLite_0.7-1
> [10] DBI_0.2-4 Biobase_2.2.0 affyio_1.10.0
>
>
> Mikko Arvas
> VTT Technical Research Centre of Finland Protein Production Team
> E-mail mikko.arvas at vtt.fi
> Phone +385-(0)40-754 1857
> Fax +358-(0)20-722 7071
> Address Tietotie 2
> PL 1000
> 02044 VTT
> Finland
> Web pages:
> VTT: www.vtt.fi
> Protein Production:
> http://www.vtt.fi/palvelut/cluster4/topic4_3/Proteiinin_tuotto.jsp
>
>
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