More importantly, how was the respective pd* (annoation) package created?
Was the NDF modified in any way? If so, how?


On 5 November 2012 17:56, P. Murakami <polyphemus421@gmail.com> wrote:

> pmChr is a function in the oligo package, not the charm package.
> Apparently your dat is not a valid TilingFeatureSet object.
>
> If you look your error message and at the definition of pmChr--type
> selectMethod(pmChr,"TilingFeatureSet")--you can see that the problem seems
> to be that your dat object has no "chrom" column in its featureSet table.
> To see this type
>
> dbGetQuery(db(dat),"SELECT * from featureSet")
>
> There should be a column named "chrom" with values for each probe like
> "chr10", "chrX", etc.
> Maybe if you study the oligo package (and maybe DBI package) more you can
> figure out how to make your dat object valid.
>
> hth
> peter
>
> On Mon, Nov 5, 2012 at 8:59 AM, Andrew Beggs <a.beggs@bham.ac.uk> wrote:
>
> > Hi****
> >
> > ** **
> >
> > It fails at the following line:****
> >
> > ** **
> >
> > chr <- pmChr(dat)****
> >
> > ** **
> >
> > And gives the error:****
> >
> > ** **
> >
> > Error in sqliteExecStatement(con, statement, bind.data) : ****
> >
> >   RS-DBI driver: (error in statement: no such column: chrom)****
> >
> > ** **
> >
> > Andrew****
> >
> > ** **
> >
> > *From:* P. Murakami [mailto:polyphemus421@gmail.com]
> > *Sent:* 02 November 2012 15:09
> > *To:* Andrew Beggs
> > *Cc:* Andrew Jaffe; Peter Murakami; bioconductor@r-project.org
> >
> > *Subject:* Re: [BioC] CHARM - The following columns in sampleKey...****
> >
> > ** **
> >
> > Try running the code inside getControlIndex and see where it fails.
> >
> > Also, "The following columns in sampleKey contain discrepant values
> > between channels and are being removed: 1" is not an error and is not
> even
> > a warning, it's just a message.  The function takes a sampleKey data
> frame
> > with 2 rows per sample and returns one (phenoData) with 1 row per sample,
> > so columns with different values in the 2 rows for the same sample can't
> be
> > included in that output data frame.  You'll always get this message for
> the
> > file name column since one row has .532 and the other has .635.
> >
> > peter murakami
> >
> > ****
> >
> > On Fri, Nov 2, 2012 at 9:54 AM, Andrew Beggs <a.beggs@bham.ac.uk>
> wrote:**
> > **
> >
> > PS I have reversed the inputs, and that looks a lot better.
> >
> > However it still fails on point 2.
> >
> > I am using the BSgenome.Hsapiens.UCSC.hg18 library - do you think that
> has
> > anything to do with it?
> >
> > A
> >
> > From: Andrew Beggs [mailto:a.beggs@bham.ac.uk]
> > Sent: 02 November 2012 13:42
> > To: Andrew Jaffe; a.beggs@bham.ac.uk; Peter Murakami;
> > bioconductor@r-project.org
> > Subject: RE: [BioC] CHARM - The following columns in sampleKey...****
> >
> >
> > Hi,
> >
> > Thanks for your help
> >
> > I have solved the first part of the puzzle, it was due to incorrect
> > conversion of the PAIR to XYS files. The other problems are
> >
> >
> > 1)      I get the following error when trying to do QC:
> >
> > > pmq= pmQuality(rawData)
> > Error in tapply(x[bgIndex, i], bgNgc, ecdf) : subscript out of bounds
> >
> >
> > 2)      I thought I had this fixed, and then got this as well when I
> tried
> > to identify unmethylated control probes:
> >
> > > ctrlIdx <- getControlIndex(rawData, subject=Hsapiens, noCpGWindow=60)
> > Error in sqliteExecStatement(con, statement, bind.data) :
> >   RS-DBI driver: (error in statement: no such column: chrom)
> >
> > I am using MeDIP as it happens, so I need to reverse the 532 and 635
> > inputs do you think? 532 is labelled as INPUT in the samplekey.txt and
> 635
> > is MBD.
> >
> > Thanks
> >
> > Andrew
> >
> >
> >
> >
> > From: Andrew Jaffe [mailto:ajaffe@jhsph.edu]
> > Sent: 02 November 2012 13:07****
> >
> > To: a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>; Peter Murakami;
> > bioconductor@r-project.org<mailto:bioconductor@r-project.org>****
> >
> > Subject: Re: [BioC] CHARM - The following columns in sampleKey...
> >
> > Hey,
> >
> > What's actual code you are running? It looks like you read the data in
> > with readCharm:
> >
> > rawData = readCharm(...)
> >
> > So is that discrepancy just a warning, and not an error?
> >
> > Also, if you are using a methyl-enrichment protocol (like MeDip) with the
> > charm package, you need to reverse the inputs - charm assumes McrBC which
> > enriches for unmethyled DNA, so the "treatment" input here would be the
> > reverse. That might be one reason why downstream analyses are failing.
> > Could you provide more code of exactly what fails later?
> >
> > Thanks,
> > Andrew Jaffe
> >
> > ------------------------------
> >
> > Message: 18
> > Date: Fri,  2 Nov 2012 01:25:08 -0700 (PDT)
> > From: "Andrew Beggs [guest]" <guest@bioconductor.org<mailto:
> > guest@bioconductor.org>>
> > To: bioconductor@r-project.org<mailto:bioconductor@r-project.org>,
> > a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>
> > Cc: charm Maintainer <pmurakam@jhsph.edu<mailto:pmurakam@jhsph.edu>>
> > Subject: [BioC] CHARM - The following columns in sampleKey...
> > Message-ID: <20121102082508.CDE081429FB@mamba.fhcrc.org<mailto:
> > 20121102082508.CDE081429FB@mamba.fhcrc.org>>
> >
> >
> > Hello
> >
> > I've being trying to get charm to read in some Nimblegen array data that
> I
> > had to convert from PAIR to XYS, also making an annotation file.
> >
> > All goes swimmingly, until I try to  use readCharm, although the data
> > appears to load, I get the following error when using readCharm:
> >
> > The following columns in sampleKey contain discrepant values between
> > channels and are being removed: 1
> >
> > It's not clear what this means, as I have looked at the two channel files
> > (532 and 635) and the structure is essentially the same. Subsequent
> > analyses fail, I assume because of missing data.
> >
> > If I look at my loaded dataset with rawData I get the following:
> >
> > > rawData
> > TilingFeatureSet (storageMode: lockedEnvironment)
> > assayData: 389307 features, 39 samples
> >   element names: channel1, channel2
> > protocolData
> >   rowNames: N3 N9 ... E2 (39 total)
> >   varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2
> >   varMetadata: labelDescription channel
> > phenoData
> >   rowNames: N3 N9 ... E2 (39 total)
> >   varLabels: sampleID tissue arrayUT arrayMD
> >   varMetadata: labelDescription channel
> > featureData: none
> > experimentData: use 'experimentData(object)'
> > Annotation: pd.2006.11.02.hg18.cpg.promo
> >
> > Can anyone help?
> >
> >  -- output of sessionInfo():
> >
> > R version 2.15.2 (2012-10-26)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> >  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> >  [7] LC_PAPER=C                 LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> >  [1] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0
> >  [3] oligoClasses_1.20.0                RSQLite_0.11.2
> >  [5] DBI_0.2-5                          charm_2.4.0
> >  [7] genefilter_1.40.0                  RColorBrewer_1.0-5
> >  [9] fields_6.7                         spam_0.29-2
> > [11] SQN_1.0.5                          nor1mix_1.1-3
> > [13] mclust_4.0                         Biobase_2.18.0
> > [15] BiocGenerics_0.4.0
> >
> > loaded via a namespace (and not attached):
> >  [1] affxparser_1.30.0     affyio_1.26.0         annotate_1.36.0
> >  [4] AnnotationDbi_1.20.2  BiocInstaller_1.8.3   Biostrings_2.26.2
> >  [7] bit_1.1-9             BSgenome_1.26.1       codetools_0.2-8
> > [10] corpcor_1.6.4         ff_2.2-9              foreach_1.4.0
> > [13] GenomicRanges_1.10.3  gtools_2.7.0          IRanges_1.16.3
> > [16] iterators_1.0.6       limma_3.14.1          MASS_7.3-22
> > [19] multtest_2.14.0       parallel_2.15.2       preprocessCore_1.20.0
> > [22] siggenes_1.32.0       splines_2.15.2        stats4_2.15.2
> > [25] survival_2.36-14      sva_3.4.0             XML_3.95-0.1
> > [28] xtable_1.7-0          zlibbioc_1.4.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org<
> > http://bioconductor.org/>.
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > http://news.gmane.org/gmane.science.biology.informatics.conductor****
> >
> > ** **
> >
>
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>
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