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
> *******************************************************************************
>
> --
> 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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>
--
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
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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