Hi Yu Chuan.
As I mentioned before, I was unable to reproduce your error from a
test dataset on my system. Its hard to know the history of your
environment, so what I suggest you do is start from a brand new
session, and run the commands start to finish. There are a couple
ways to do this. By brut strength, you could delete the relevant
plmData/ and probeData/ directories and when you run the commands,
aroma.affymetrix will just recreate them. Alternatively (and more
elegantly?), you can add a 'force=TRUE' argument to all the process()
and fit() commands that you use.
Hope that helps.
Cheers,
Mark
On 2-Dec-09, at 11:59 AM, Yu Chuan wrote:
> Mark,
>
> I pulled out some chip effects....the NUSE are still all 0s.
>
>> cesTr <- getChipEffectSet(plmTr)
>>
>> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
>> dim(trFit)
> [1] 3 13
>> trFit
> unitName groupName unit group cell 20091119_Colon4_Exon2
> 1 2315251 2315252 1 1 1 21.13534
> 2 2315373 2315374 2 1 3 21.74671
> 3 2315554 2315586 3 1 7 22.94160
> 20091119_Colon4_Exon3 20091119_UBR_Exon1 20091119_UBR_Exon2
> 1 22.23353 21.05928 21.57542
> 2 21.51784 21.39991 22.58863
> 3 22.78790 22.42114 23.21064
> 20091119_UBR_Exon3 20091119_UHR_Exon1 20091119_UHR_Exon2
> 20091119_UHR_Exon3
> 1 21.29856 22.37293 22.17496
> 21.97057
> 2 21.72278 22.74162 22.76515
> 22.23168
> 3 22.39577 23.52349 23.74061
> 22.97983
>
>> qamTr <- QualityAssessmentModel(plmTr)
>>
>> z <- plotNuse(qamTr)
>> z
> $`20091119_Colon4_Exon2`
> $`20091119_Colon4_Exon2`$stats
> [1] 0 0 0 0 0
>
> $`20091119_Colon4_Exon2`$n
> [1] 18705
>
> $`20091119_Colon4_Exon2`$conf
> [1] 0 0
>
> $`20091119_Colon4_Exon2`$out
> numeric(0)
>
>
> $`20091119_Colon4_Exon3`
> $`20091119_Colon4_Exon3`$stats
> [1] 0 0 0 0 0
>
> $`20091119_Colon4_Exon3`$n
> [1] 18705
>
> $`20091119_Colon4_Exon3`$conf
> [1] 0 0
>
> $`20091119_Colon4_Exon3`$out
> numeric(0)
>
>
> $`20091119_UBR_Exon1`
> $`20091119_UBR_Exon1`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UBR_Exon1`$n
> [1] 18705
>
> $`20091119_UBR_Exon1`$conf
> [1] 0 0
>
> $`20091119_UBR_Exon1`$out
> numeric(0)
>
>
> $`20091119_UBR_Exon2`
> $`20091119_UBR_Exon2`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UBR_Exon2`$n
> [1] 18705
>
> $`20091119_UBR_Exon2`$conf
> [1] 0 0
>
> $`20091119_UBR_Exon2`$out
> numeric(0)
>
>
> $`20091119_UBR_Exon3`
> $`20091119_UBR_Exon3`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UBR_Exon3`$n
> [1] 18705
>
> $`20091119_UBR_Exon3`$conf
> [1] 0 0
>
> $`20091119_UBR_Exon3`$out
> numeric(0)
>
>
> $`20091119_UHR_Exon1`
> $`20091119_UHR_Exon1`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UHR_Exon1`$n
> [1] 18705
>
> $`20091119_UHR_Exon1`$conf
> [1] 0 0
>
> $`20091119_UHR_Exon1`$out
> numeric(0)
>
>
> $`20091119_UHR_Exon2`
> $`20091119_UHR_Exon2`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UHR_Exon2`$n
> [1] 18705
>
> $`20091119_UHR_Exon2`$conf
> [1] 0 0
>
> $`20091119_UHR_Exon2`$out
> numeric(0)
>
>
> $`20091119_UHR_Exon3`
> $`20091119_UHR_Exon3`$stats
> [1] 0 0 0 0 0
>
> $`20091119_UHR_Exon3`$n
> [1] 18705
>
> $`20091119_UHR_Exon3`$conf
> [1] 0 0
>
> $`20091119_UHR_Exon3`$out
> numeric(0)
>
>
> attr(,"type")
> [1] "NUSE"
>
>
> On Nov 30, 1:28 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>> Hi Yu Chuan.
>>
>> I'm still mystified by this. Can you check that the PLM was
>> successfully fit? Pull out some chip effects, maybe.
>>
>> Cheers,
>> Mark
>>
>> On 25-Nov-09, at 4:51 AM, Yu Chuan wrote:
>>
>>
>>
>>> Mark,
>>
>>> I think the below info. may help too. Looks like all the gene-level
>>> NUSE are 0. How could this happen?
>>
>>> z <- plotNuse(qamTr)
>>>> z
>>> $`20091119_Colon4_Exon2`
>>> $`20091119_Colon4_Exon2`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_Colon4_Exon2`$n
>>> [1] 18705
>>
>>> $`20091119_Colon4_Exon2`$conf
>>> [1] 0 0
>>
>>> $`20091119_Colon4_Exon2`$out
>>> numeric(0)
>>
>>> $`20091119_Colon4_Exon3`
>>> $`20091119_Colon4_Exon3`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_Colon4_Exon3`$n
>>> [1] 18705
>>
>>> $`20091119_Colon4_Exon3`$conf
>>> [1] 0 0
>>
>>> $`20091119_Colon4_Exon3`$out
>>> numeric(0)
>>
>>> $`20091119_UBR_Exon1`
>>> $`20091119_UBR_Exon1`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UBR_Exon1`$n
>>> [1] 18705
>>
>>> $`20091119_UBR_Exon1`$conf
>>> [1] 0 0
>>
>>> $`20091119_UBR_Exon1`$out
>>> numeric(0)
>>
>>> $`20091119_UBR_Exon2`
>>> $`20091119_UBR_Exon2`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UBR_Exon2`$n
>>> [1] 18705
>>
>>> $`20091119_UBR_Exon2`$conf
>>> [1] 0 0
>>
>>> $`20091119_UBR_Exon2`$out
>>> numeric(0)
>>
>>> $`20091119_UBR_Exon3`
>>> $`20091119_UBR_Exon3`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UBR_Exon3`$n
>>> [1] 18705
>>
>>> $`20091119_UBR_Exon3`$conf
>>> [1] 0 0
>>
>>> $`20091119_UBR_Exon3`$out
>>> numeric(0)
>>
>>> $`20091119_UHR_Exon1`
>>> $`20091119_UHR_Exon1`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UHR_Exon1`$n
>>> [1] 18705
>>
>>> $`20091119_UHR_Exon1`$conf
>>> [1] 0 0
>>
>>> $`20091119_UHR_Exon1`$out
>>> numeric(0)
>>
>>> $`20091119_UHR_Exon2`
>>> $`20091119_UHR_Exon2`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UHR_Exon2`$n
>>> [1] 18705
>>
>>> $`20091119_UHR_Exon2`$conf
>>> [1] 0 0
>>
>>> $`20091119_UHR_Exon2`$out
>>> numeric(0)
>>
>>> $`20091119_UHR_Exon3`
>>> $`20091119_UHR_Exon3`$stats
>>> [1] 0 0 0 0 0
>>
>>> $`20091119_UHR_Exon3`$n
>>> [1] 18705
>>
>>> $`20091119_UHR_Exon3`$conf
>>> [1] 0 0
>>
>>> $`20091119_UHR_Exon3`$out
>>> numeric(0)
>>
>>> attr(,"type")
>>> [1] "NUSE"
>>
>>> On Nov 24, 9:32 am, Yu Chuan <mbc...@gmail.com> wrote:
>>>> Hi Mark,
>>
>>>> Thanks for your prompt reply. Below is my complete R code together
>>>> with error information. I tried what you suggested, but the
>>>> resulted
>>>> NUSE plot still looks the same.
>>>> Also, what does it mean if the boxplot for a chip's exon-level NUSE
>>>> suggests that this chip maybe an outlier (i.e. the median is higher
>>>> than those of other chips), while its RLE boxplot doesn't suggest
>>>> that
>>>> (its RLE boxplot align with others)? Should I treat this chip as an
>>>> outlier at all?
>>
>>>> Another question I have been puzzled was:
>>>> I noticed that exon-level NUSE boxplots typically show higher
>>>> heterogeneity across chips, while gene-level NUSE boxplots don't.
>>>> And
>>>> RLE boxplots don't show much heterogeneity either at the exon-level
>>>> or
>>>> gene-level. Could someone give me an idea about why this is the
>>>> case,
>>>> and whether I should define an outlier based on the gene-level or
>>>> exon-
>>>> level NUSE/RLE?
>>
>>>> Thanks!
>>>> Yu Chuan
>>
>>>>> chipType <- "HuEx-1_0-st-v2"
>>
>>>>> # use EP's custom CDF
>>>>> cdf <- AffymetrixCdfFile$byChipType(chipType,
>>>>> tags="coreR3,A20071112,EP")
>>
>>>>> print(cdf)
>>
>>>> AffymetrixCdfFile:
>>>> Path: annotationData/chipTypes/HuEx-1_0-st-v2
>>>> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>>>> Filesize: 38.25MB
>>>> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>>>> RAM: 0.00MB
>>>> File format: v4 (binary; XDA)
>>>> Dimension: 2560x2560
>>>> Number of cells: 6553600
>>>> Number of units: 18708
>>>> Cells per unit: 350.31
>>>> Number of QC units: 1
>>
>>>>> cs <- AffymetrixCelSet$byName("PilotStudy", cdf=cdf)
>>>>> bc <- RmaBackgroundCorrection(cs, tag="coreR3")
>>>>> csBC <- process(bc,verbose=verbose)
>>
>>>> Background correcting data set...
>>>> Already background corrected
>>>> Background correcting data set...done
>>
>>>>> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>>
>>>>> csN <- process(qn, verbose=verbose)
>>
>>>> Quantile normalizing data set...
>>>> Already normalized
>>>> Quantile normalizing data set...done
>>
>>>>> 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: PilotStudy
>>>> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>>>> Input tags: coreR3,QN
>>>> Output tags: coreR3,QN,RMA,merged
>>>> Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
>>>> "affyPLM"; treatNAsAs: chr "weights"; mergeGroups: logi TRUE).
>>>> Path: plmData/PilotStudy,coreR3,QN,RMA,merged/HuEx-1_0-st-v2
>>>> RAM: 0.00MB
>>>> Identifying non-estimated units...
>>>> Identifying non-estimated units...done
>>>> Getting model fit for 0 units.
>>>> Fitting model of class ExonRmaPlm:...done> fit(plmEx,
>>>> verbose=verbose)
>>
>>>> Fitting model of class ExonRmaPlm:...
>>>> ExonRmaPlm:
>>>> Data set: PilotStudy
>>>> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>>>> Input tags: coreR3,QN
>>>> Output tags: coreR3,QN,RMA
>>>> Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
>>>> "affyPLM"; treatNAsAs: chr "weights"; mergeGroups: logi FALSE).
>>>> Path: plmData/PilotStudy,coreR3,QN,RMA/HuEx-1_0-st-v2
>>>> RAM: 0.00MB
>>>> Identifying non-estimated units...
>>>> Identifying non-estimated units...done
>>>> Getting model fit for 0 units.
>>>> Fitting model of class ExonRmaPlm:...done> qamTr <-
>>>> QualityAssessmentModel(plmTr)
>>>>> plotNuse(qamTr)
>>>>> plotRle(qamTr)
>>
>>>> Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs =
>>>> pars
>>>> $yaxs) :
>>>> need finite 'ylim' values
>>>> In addition: There were 16 warnings (use warnings() to see them)>
>>>> qamEx <- QualityAssessmentModel(plmEx)
>>>>> plotNuse(qamEx)
>>>>> plotRle(qamEx)
>>>>> z <- plotNuse(qamTr)
>>>>> plotBoxplotStats(z, ylim=c(-0.01,0.01))
>>>>> sessionInfo()
>>
>>>> R version 2.9.2 (2009-08-24)
>>>> i386-pc-mingw32
>>
>>>> locale:
>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>>> States.
>>>> 1252;LC_MONETARY=English_United States.
>>>> 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods
>>>> base
>>
>>>> other attached packages:
>>>> [1] aroma.affymetrix_1.2.0 aroma.apd_0.1.6
>>>> affxparser_1.16.0
>>>> [4] R.huge_0.1.9 aroma.core_1.2.0
>>>> aroma.light_1.12.2
>>>> [7] matrixStats_0.1.6 R.rsp_0.3.6
>>>> R.filesets_0.5.3
>>>> [10] digest_0.4.1 R.cache_0.1.9
>>>> R.utils_1.2.0
>>>> [13] R.oo_1.5.0 R.methodsS3_1.0.3> traceback()
>>
>>>> 8: plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
>>>> $yaxs)
>>>> 7: bxp(bxpStats, ylim = ylim, outline = outline, las = las, ...)
>>>> 6: plotBoxplotStats.list(stats, main = main, ylab = ylab, ...)
>>>> 5: plotBoxplotStats(stats, main = main, ylab = ylab, ...)
>>>> 4: plotBoxplot.ChipEffectSet(ces, type = "RLE", ...)
>>>> 3: plotBoxplot(ces, type = "RLE", ...)
>>>> 2: plotRle.QualityAssessmentModel(qamTr)
>>>> 1: plotRle(qamTr)
>>
>>>> On Nov 24, 1:50 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>>
>>>>> Hi Yu Chuan.
>>
>>>>> Comments below.
>>
>>>>> On 24-Nov-09, at 1:00 PM, Yu Chuan wrote:
>>
>>>>>> Hi,
>>
>>>>>> I am pre-processing 8 exon arrays (Hu-Ex-1_0-st-v2) and doing
>>>>>> quality
>>>>>> assessment. When I plotted the NUSE using plotNUSE, I found that
>>>>>> the
>>>>>> y-
>>>>>> axis limit is too wide, such that the boxplots were all squeezed
>>>>>> tightly around 0 and it's hard to see what's going on there. Is
>>>>>> there
>>>>>> any way I can change the y-axis limit? I tried
>>
>>>>> I assume you mean tightly around 1? That's where they should be.
>>
>>>>>>> plotNuse(qamTr,ylim=c(-0.2,0.2))
>>>>>> Error in boxplot.stats(stdvs/medianSE, ...) :
>>>>>> unused argument(s) (ylim = c(-0.2, 0.2))
>>
>>>>> An easy work-around for this is:
>>
>>>>> z <- plotNuse(qamTr)
>>>>> plotBoxplotStats(z, ylim=c(.5,2))
>>
>>>>> I'm unable to recreate these errors below on a local dataset.
>>>>> They
>>>>> all work fine for me. Here is my complete set of commands from a
>>>>> fresh R session, as described in the exon array vignette page:
>>
>>>>> http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-
>>>>> ...
>>
>>>>> ----------------
>>>>> library(aroma.affymetrix)
>>>>> cdf <- AffymetrixCdfFile$byChipType(chipType,
>>>>> tags="coreR3,A20071112,EP")
>>>>> cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
>>>>> setCdf(cs,cdf)
>>
>>>>> bc <- RmaBackgroundCorrection(cs, tag="coreR2")
>>>>> csBC <- process(bc,verbose=verbose)
>>
>>>>> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>>>>> csN <- process(qn, verbose=verbose)
>>
>>>>> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
>>>>> fit(plmTr, verbose=verbose)
>>
>>>>> rs <- calculateResiduals(plmTr, verbose=verbose)
>>>>> qamTr <- QualityAssessmentModel(plmTr)
>>>>> plotNuse(qamTr)
>>
>>>>> z <- plotNuse(qamTr)
>>>>> plotBoxplotStats(z, ylim=c(.5,2))
>>
>>>>> plotRle(z)
>>>>> ----------------
>>
>>>>> Have you fit the probe level model in advance of these commands?
>>>>> Given that your NUSE values are tightly around 0, I suspect maybe
>>>>> not. Otherwise, can you give a complete code example, and maybe
>>>>> run
>>>>> it from a fresh R session and check whether that solves your
>>>>> problem.
>>>>> And, as usual, if you get an error, the output of traceback() is
>>>>> much
>>>>> appreciated ... and of course, the output of your sessionInfo().
>>
>>>>> Hope that helps.
>>
>>>>> Cheers,
>>>>> Mark
>>
>>>>> ps. my sessionInfo():
>>
>>>>> > sessionInfo()
>>>>> R version 2.10.0 (2009-10-26)
>>>>> i386-apple-darwin9.8.0
>>
>>>>> locale:
>>>>> [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods
>>>>> base
>>
>>>>> other attached
>>
>> ...
>>
>> read more ยป- Hide quoted text -
>>
>> - Show quoted text -
>
> --
> 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
------------------------------
--
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
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