Hi Zaid.
Another thing to check/report in your next update (after you update to
the new aroma.affymetrix) is whether you have reasonable chip
effects. This is what Henrik was eluding to in his last comment.
bxp() which is eventually called by plotRle() will handle NAs, so that
shouldn't be the problem. The thing it won't handle is if *all*
values are NA or all equal to the same number e.g. 0. I seem to
recall you had this issue before. For example, what does these
commands give:
[...all your previous stuff...]
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
head(trFit)
One thing that worries/interests me is your comment "I tried to use
less CEL files and as few as 3". I've run plotRle() on 10s of samples
and I suspect that is not the problem. Can you explain exactly what
you tried?
And, if not too much work, it may even be best to create a completely
new directory as if you were starting from scratch (say, with a
handful of files), run your entire script and report back.
Cheers,
Mark
On 25-Feb-10, at 8:19 AM, Henrik Bengtsson wrote:
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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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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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
______________________________________________________________________
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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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