Hello,
Please see below the requested information:
1. > sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.6.0 affxparser_1.30.0 aroma.apd_0.2.3
[4] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.6.0
[7] matrixStats_0.6.2 R.rsp_0.8.2 R.cache_0.6.5
[10] R.devices_2.1.1 R.filesets_1.6.0 digest_0.5.2
[13] R.utils_1.18.0 R.oo_1.10.1 R.methodsS3_1.4.2
2. The script (up to the point where I get the error) (sorry it does not
work to attach files so I am pasting it in here):
library("aroma.affymetrix")
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
options(digits=4)
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
print(cdf)
gi <- getGenomeInformation(cdf)
print(gi)
si <- getSnpInformation(cdf)
print(si)
acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
print(acs)
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
csR <- AffymetrixCelSet$byName("test", cdf=cdf)
print(csR)
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
print(acc)
csC <- process(acc, verbose=verbose)
print(csC)
bpn <- BasePositionNormalization(csC, target="zero")
print(bpn)
csN <- process(bpn, verbose=verbose)
print(csN)
plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
print(plm)
if (length(findUnitsTodo(plm)) > 0) {
# Fit CN probes quickly (~5-10s/array + some overhead)
units <- fitCnProbes(plm, verbose=verbose)
str(units)
# int [1:945826] 935590 935591 935592 935593 935594 935595 ...
# Fit remaining units, i.e. SNPs (~5-10min/array)
units <- fit(plm, verbose=verbose) # <--- error here
str(units)
}
3. > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
Thank you!
On Monday, 26 November 2012 17:52:39 UTC+2, Henrik Bengtsson wrote:
>
> Hi,
>
> please provide the following information so I can help troubleshoot:
>
> 1. What's your sessionInfo() after doing library("aroma.affymetrix")?
>
> 2. Your complete script (right now I not sure which chip type your are
> working on) up to the point where you get the error.
>
> 3. The output of print(cdf) where 'cdf' is your AffymetrixCdfFile object.
>
> Henrik
>
> On Mon, Nov 26, 2012 at 7:40 AM, Ioana Cutcutache
> <ioana.cu...@gmail.com <javascript:>> wrote:
> > Hello,
> >
> > I am trying to use CRMA v2 and basically just following the instructions
> at
> > http://www.aroma-project.org/vignettes/CRMAv2.
> > I have all the annotation files and I think everything is right (the
> > checking of this files gives me the same output as the webpage mentioned
> > above).
> > However when I get to
> > units <- fit(plm, verbose=verbose)
> > I get the following error which I am no able to solve:
> >
> > [... removed output...]
> > 20121126 19:51:39| Setting up parameter sets...done
> > 20121126 19:51:39| Fitting AvgCnPlm for each unit type separately...
> > 20121126 19:51:39| Unit types:
> > unknown expression genotyping
> > 0 1 2
> > 20121126 19:51:39| Unit type #1 ('unknown') of 3...
> > 20121126 19:51:39| Unit type: unknown (code=0)
> > 20121126 19:51:39| Number of units of this type: 1590374
> > int [1:1590374] 291042 291043 291044 291045 291046 291047 291048
> > 291049 291050 291051 ...
> > 20121126 19:51:39| Fitting the model by unit dimensions (at least
> > for the large classes)...
> > 20121126 19:51:39| Grouping units into equivalent (unit,group,cell)
> > dimensions...
> > [2012-11-26 19:51:39] Exception: Argument 'units' contains 25346 NA
> > value(s).
> >
> > at #11. getNumerics.Arguments(static, ..., asMode = "integer",
> > disallow = disallow)
> > - getNumerics.Arguments() is in environment 'R.utils'
> >
> > at #10. getNumerics(static, ..., asMode = "integer", disallow =
> disallow)
> > - getNumerics() is in environment 'R.utils'
> >
> > at #09. getIntegers.Arguments(static, x, ..., range = range, .name =
> > .name)
> > - getIntegers.Arguments() is in environment 'R.utils'
> >
> > at #08. getIntegers(static, x, ..., range = range, .name = .name)
> > - getIntegers() is in environment 'R.utils'
> >
> > at #07. getIndices.Arguments(static, ...)
> > - getIndices.Arguments() is in environment 'R.utils'
> >
> > at #06. getIndices(static, ...)
> > - getIndices() is in environment 'R.utils'
> > - originating from '<text>'
> >
> > at #05. Arguments$getIndices(units, max = nbrOfUnits(this))
> > - Arguments$getIndices() is local of the calling function
> >
> > at #04. groupUnitsByDimension.AffymetrixCdfFile(cdf, units = unitsTT,
> > verbose = less(verbose, 50))
> > - groupUnitsByDimension.AffymetrixCdfFile() is in
> > environment 'aroma.affymetrix'
> >
> > at #03. groupUnitsByDimension(cdf, units = unitsTT, verbose =
> > less(verbose,
> > 50))
> > - groupUnitsByDimension() is in environment 'aroma.affymetrix'
> >
> > at #02. fit.ProbeLevelModel(plm, verbose = verbose)
> > - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
> >
> > at #01. fit(plm, verbose = verbose)
> > - fit() is in environment 'aroma.core'
> >
> > Error: Argument 'units' contains 25346 NA value(s).
> > 20121126 19:51:39| Grouping units into equivalent (unit,group,cell)
> > dimensions...done
> > 20121126 19:51:39| Fitting the model by unit dimensions (at least
> > for the large classes)...done
> > 20121126 19:51:39| Unit type #1 ('unknown') of 3...done
> > 20121126 19:51:39| Fitting AvgCnPlm for each unit type separately...done
> > 20121126 19:51:39|Fitting model of class AvgCnPlm...done
> >
> > Does anybody know what might be causing this error?
> >
> > Thank you!
> >
> > --
> > 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
> > aroma-af...@googlegroups.com<javascript:>
> > 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.
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