Ok, before we try to troubleshoot this one, please update to the
latest aroma.affymetrix version. The one you are using is nearly
three months old, and I prefer to troubleshoot the current code base.
When you've done that, it should be enough to run plotRle(); you don't
have to rerun everything.
BTW, did you remember to call fit() on the probe-level model?
On Wed, Feb 24, 2010 at 8:15 PM, zaid z...@genomedx.com wrote:
8: plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs)
7: bxp(bxpStats, ylim = ylim, outline = outline, las = las, ...)
6: plotBoxplotStats.list(stats, main = main, ylab = ylab, ...)
5: plotBoxplotStats(stats, main = main, ylab = ylab, ...)
4: plotBoxplot.ChipEffectSet(ces, type = RLE, ...)
3: plotBoxplot(ces, type = RLE, ...)
Chip type: HuEx-1_0-st-v2,monocell
Number of arrays: 2
Names: S370-A-HuEx-1_0-st-v2-01-1 (S09-13138), S371-A-HuEx-1_0-st-
Time period: 2010-02-24 10:28:31 -- 2010-02-24 10:28:31
Total file size: 5.43MB
Parameters: (probeModel: chr pm, mergeGroups: logi TRUE)
R version 2.10.0 (2009-10-26)
 LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
 LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
 stats graphics grDevices utils datasets methods
other attached packages:
 Biobase_2.6.0 aroma.affymetrix_1.3.0
 R.huge_0.2.0 aroma.core_1.3.1
 R.rsp_0.3.6 R.filesets_0.6.5
 R.utils_1.2.4 R.oo_1.6.5
loaded via a namespace (and not attached):
 affyio_1.14.0 preprocessCore_1.8.0
How can i get more details on the error.
I tried to use less CEL files and as few as 3, still no luck.
Thanks in advance
On Feb 24, 10:46 am, Henrik Bengtsson henrik.bengts...@gmail.com
there are probably more output from the error, or ? If so, could you
please provide us with that one? Also, whenever you get an error, is
it is always helpful to report output of traceback() [see email
What's your sessionInfo()?
On Wed, Feb 24, 2010 at 7:29 PM, zaid z...@genomedx.com wrote:
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
NAs not allowed in 'ylim'
On Feb 24, 10:19 am, zaid z...@genomedx.com wrote:
I was doing QC analysis in aroma in R on HuEx chip but got an error
while trying to plot NUSE.
ylim contains NA.
I'm running R 2.10(32bit) on a windows 7(64bit).
verbose - Arguments$getVerbose(-8, timestamp=TRUE)
chipType - HuEx-1_0-st-v2
cdf - AffymetrixCdfFile$byChipType(chipType)
cs - AffymetrixCelSet$byName(tissues, cdf=cdf)
bc - RmaBackgroundCorrection(cs)
csBC - process(bc,verbose=verbose)
qn - QuantileNormalization(csBC, typesToUpdate=pm)
csN - process(qn, verbose=verbose)
plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)
qamTr - QualityAssessmentModel(plmTr)
End of command
I was able to run the previous on U95A data and Plus 2 data. Also, in
the past I was able to run that on HuEx data.
The cdf file I'm using is binary and used multiples ones (HuEx-1_0-
v2,extended,A20071112,EP.cdf etc offered on Elizabeth's
Could you please point me how to fix this problem?
Thanks in advance
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