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.
>
>
> You received this message because you are subscribed to the Google  
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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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