[aroma.affymetrix] error with fit() Mouse Exon

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[aroma.affymetrix] error with fit() Mouse Exon

Richard Beyer
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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Re: [aroma.affymetrix] error with fit() Mouse Exon

Henrik Bengtsson-4
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 <[hidden email]> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> 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 "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] error with fit() Mouse Exon

Richard Beyer
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 <[hidden email]> 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 <[hidden email]> 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.
>
>
> You received this message because you are subscribed to the Google Groups
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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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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/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/