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?
/Henrik
On Wed, Feb 24, 2010 at 8:15 PM, zaid z...@genomedx.com wrote:
traceback()
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, ...)
2: plotRle.QualityAssessmentModel(qamTr)
1: plotRle(qamTr)
qamTr
QualityAssessmentModel:
Name: tissues
Tags: RBC,QN,RMA,merged,QC
Path: qcData/tissues,RBC,QN,RMA,merged,QC/HuEx-1_0-st-v2
Chip-effect set:
ExonChipEffectSet:
Name: tissues
Tags: RBC,QN,RMA,merged
Path: plmData/tissues,RBC,QN,RMA,merged/HuEx-1_0-st-v2
Platform: Affymetrix
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-
v2-01-1 (S09-07848)
Time period: 2010-02-24 10:28:31 -- 2010-02-24 10:28:31
Total file size: 5.43MB
RAM: 0.01MB
Parameters: (probeModel: chr pm, mergeGroups: logi TRUE)
RAM: 0.00MB
sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] Biobase_2.6.0 aroma.affymetrix_1.3.0
aroma.apd_0.1.7 affxparser_1.18.0
[5] R.huge_0.2.0 aroma.core_1.3.1
aroma.light_1.15.1 matrixStats_0.1.8
[9] R.rsp_0.3.6 R.filesets_0.6.5
digest_0.4.1 R.cache_0.2.0
[13] R.utils_1.2.4 R.oo_1.6.5
affy_1.24.2 R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] 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
wrote:
Hi,
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
footer].
What's your sessionInfo()?
/Henrik
On Wed, Feb 24, 2010 at 7:29 PM, zaid z...@genomedx.com wrote:
Error:
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
$yaxs) :
NAs not allowed in 'ylim'
On Feb 24, 10:19 am, zaid z...@genomedx.com wrote:
I was doing QC analysis in aroma in R on HuEx chip but got an error
while trying to plot NUSE.
ylim contains NA.
I'm running R 2.10(32bit) on a windows 7(64bit).
my command:
library(aroma.affymetrix)
verbose - Arguments$getVerbose(-8, timestamp=TRUE)
chipType - HuEx-1_0-st-v2
cdf - AffymetrixCdfFile$byChipType(chipType)
print(cdf)
cs - AffymetrixCelSet$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)
fit(plmTr, verbose=verbose)
qamTr - QualityAssessmentModel(plmTr)
plotNuse(qamTr)
plotRle(qamTr)
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-
st-
v2,core,A20071112,EP.cdf, HuEx-1_0-st-
v2,control,A20071112,EP.cdf, HuEx-1_0-st-
v2,extended,A20071112,EP.cdf etc offered on Elizabeth's
Columnhttp://groups.google.com/group/aroma-affymetrix/web/affymetrix-define...
)
Could you please point me how to fix this problem?
Thanks in advance
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