Hi Henrik,
Thanks very much for your excellent help. Your suggestion of re-downloading
solved the problem. In the future I'll try to be more complete in my
explanation so I don;t make tracking down the problem more difficult than it
has to be :-)
Thanks much,
Dick
On Wed, Nov 17, 2010 at 7:11 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Hi,
>
> I suspect that you have an incomplete CDF file, e.g. due to
> downloading errors. Verify that you get the same output as the
> following:
>
> > print(cdf);
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
> Filename: MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
> Filesize: 176.32MB
> Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 265508
> Cells per unit: 24.68
> Number of QC units: 1
>
> Especially the following:
>
> > print(getFileSize(cdf));
> [1] 184886673
> > print(getChecksum(cdf));
> [1] "462897c4c2703764e075c945118f8c1a"
> > stopifnot(getChecksum(cdf) == "462897c4c2703764e075c945118f8c1a");
> >
>
> If that is not the case, download the file again.
>
> Then continue with the following, which is what is happening
> internally when you get the error message:
>
> > cdfM <- getMonocellCdf(cdf, verbose=-5);
> Retrieving monocell CDF...
> Monocell chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR,monocell
> Locating monocell CDF...
> Pathname:
> Locating monocell CDF...done
> Could not locate monocell CDF. Will create one for chip type...
> Creating monocell CDF...
> Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR
> Output pathname (temporary):
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0
> -st-v1,fullR1,A20080718,MR,monocell.CDF.tmp
> Number of cells per group field: 1
> Reading CDF group names...
> [...]
> Creating monocell CDF...done
> Could not locate monocell CDF. Will create one for chip type...done
> Retrieving monocell CDF...done
> >
>
> If you get this far without errors, things will work.
>
> Before restarting the analysis (your script), you need to delete all
> previous intermediate results, that is all subdirectories in
> probeData/ and plmData/ with names starting with
> HevnerMouseEx_10.11.16.
>
> Also, just in case, clear the memoization cache as follows:
>
> > library("R.utils");
> > path <- file.path(getCacheRootPath(), "aroma.affymetrix",
> "MoEx-1_0-st-v1");
> > unlink(path.expand(path), recursive=TRUE);
>
> /Henrik
>
>
> On Wed, Nov 17, 2010 at 4:33 PM, Richard Beyer <rpbe...@gmail.com> wrote:
> > Hi,
> >
> > I am following the example for low level analysis for Human Exon arrays:
> >
> > http://www.aroma-project.org/node/37
> >
> > I downloaded all the appropriate cdf files from:
> >
> > http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
> >
> > All the commands in the Vignette work fine until fit()
> >
> > chipType <- "MoEx-1_0-st-v1"
> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="fullR1,A20080718,MR")
> > print(cdf)
> > getPathname(cdf)
> > cs <- AffymetrixCelSet$byName("HevnerMouseEx_10.11.16", cdf=cdf)
> > setCdf(cs,cdf)
> > bc <- RmaBackgroundCorrection(cs, tag="fullR1")
> > csBC <- process(bc,verbose=verbose)
> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> > print(qn)
> > csN <- process(qn, verbose=verbose)
> > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
> > print(plmTr)
> > plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE)
> > print(plmEx)
> > fit(plmTr, verbose=verbose)
> >
> > Fitting model of class ExonRmaPlm...
> > ExonRmaPlm:
> > Data set: HevnerMouseEx_10.11.16
> > Chip type: MoEx-1_0-st-v1,fullR1,A20080718,MR
> > Input tags: fullR1,QN
> > Output tags: fullR1,QN,RMA,merged
> > Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr "affyPLM";
> > treatNAsAs: chr "weights"; mergeGroups: logi TRUE).
> > Path: plmData/HevnerMouseEx_10.11.16,fullR1,QN,RMA,merged/MoEx-1_0-st-v1
> > RAM: 0.00MB
> > Identifying non-estimated units...
> > Writes CDF header and unit names...
> > Writes CDF header and unit names...done
> > Writes QC units...
> > Units left: 0
> > Writes QC units...done
> > Writes 11415 units...
> > Units left: 10415, 9415, 8415, 7415, 6415, 5415, 4415, 3415, 2415,
> 1415,
> > 415, 0
> > Writes 11415 units...done
> >
> > <snip>
> >
> > Writes 11415 units...
> > Units left: 10415, 9415, 8415, 7415, 6415, 5415, 4415, 3415, 2415,
> 1415,
> > 415, 0
> > Writes 11415 units...done
> > Writes 2963 units...
> > Units left: 1963, 963, 0
> > Writes 2963 units...done
> > Error in list(`fit(plmTr, verbose = verbose)` = <environment>,
> > `fit.ProbeLevelModel(plmTr, verbose = verbose)` = <environment>, :
> >
> > [2010-11-17 14:40:04] Exception: Failed to create a valid mono-cell CDF:
> The
> > cell indices are not contiguous: 1, -913715, 0, 21002, -21002, 31326208,
> > -31326207, 31326207, -31326208, 739252, -738296, 31812, -32768, 913720,
> > -913719, -1, 955, 244737, -245692, -31325951, -257, 19196744, -19196744,
> > 745944, -744988, 913727, -913726, 752636, -751680, 913734, -913733,
> 759328,
> > -758372, 913741, -913740, 766020, -765064, 913748, -913747, 772712,
> -772709,
> > 244733, -244736, 5036, -5036, 2873, -2873, 3
> > at throw(Exception(...))
> > at throw.default("Failed to create a valid mono-cell CDF: The cell
> indices
> > are not contiguous: ", paste(udcells, collapse = ", "))
> > at throw("Failed to create a valid mono-cell CDF: The cell indices are
> not
> > contiguous: ", paste(udcells, collapse = ", "))
> > at createMonocellCdf.AffymetrixCdfFile(this, ..., verbose =
> less(verbose))
> > at createMonocellCdf(this, ..., verbose = less(verbose))
> > at getMonocellCdf.AffymetrixCdfFile(cdf, ..., verbose = less(verbose))
> >
> > Identifying non-estimated units...done
> > Fitting model of class ExonRmaPlm...done
> >> sessionInfo()
> > R version 2.12.0 (2010-10-15)
> > Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
> > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
> > LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics grDevices datasets utils methods base
> >
> > other attached packages:
> > [1] preprocessCore_1.12.0 affyio_1.18.0 Biobase_2.10.0
> > aroma.affymetrix_1.8.0 aroma.apd_0.1.7 affxparser_1.22.0
> > [7] R.huge_0.2.0 aroma.core_1.8.0 aroma.light_1.18.2
> > matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0
> > [13] R.filesets_0.9.0 digest_0.4.2 R.utils_1.5.7
> > R.oo_1.7.4 affy_1.28.0 R.methodsS3_1.2.1
> >
> > I just rev'ed to 2.12.0 and updated packages(). If anyone had a
> suggestion
> > I would be very grateful.
> >
> > Thanks very much,
> > Dick
> >
> *******************************************************************************
> > Richard P. Beyer, Ph.D. University of Washington
> > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
> > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
> > Seattle, WA 98105-6099
> > http://depts.washington.edu/ceeh/members_fc_bioinfo.html
> > http://staff.washington.edu/~dbeyer<http://staff.washington.edu/%7Edbeyer>
> >
> *******************************************************************************
> >
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
> >
> >
> > You received this message because you are subscribed to the Google Groups
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> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe and other options, go to
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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