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 packages:
>>> [1] preprocessCore_1.7.9 Biobase_2.5.8
>>> aroma.affymetrix_1.2.0
>>> [4] aroma.apd_0.1.7 affxparser_1.17.5 R.huge_0.2.0
>>> [7] aroma.core_1.2.0 aroma.light_1.13.5
>>> matrixStats_0.1.6
>>> [10] R.rsp_0.3.6 R.filesets_0.5.3 digest_0.4.1
>>> [13] R.cache_0.2.0 R.utils_1.2.2 R.oo_1.6.2
>>> [16] affy_1.23.12 R.methodsS3_1.0.3
>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.13.5
>>
>>>> But it didn't work. In addition, I got the following error when I
>>>> used
>>>> plotRLE
>>
>>>> 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)
>>>>> warnings()
>>>> Warning messages:
>>>> 1: In min(x) : no non-missing arguments to min; returning Inf
>>>> 2: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 3: In min(x) : no non-missing arguments to min; returning Inf
>>>> 4: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 5: In min(x) : no non-missing arguments to min; returning Inf
>>>> 6: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 7: In min(x) : no non-missing arguments to min; returning Inf
>>>> 8: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 9: In min(x) : no non-missing arguments to min; returning Inf
>>>> 10: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 11: In min(x) : no non-missing arguments to min; returning Inf
>>>> 12: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 13: In min(x) : no non-missing arguments to min; returning Inf
>>>> 14: In max(x) : no non-missing arguments to max; returning -Inf
>>>> 15: In min(x) : no non-missing arguments to min; returning Inf
>>>> 16: In max(x) : no non-missing arguments to max; returning -Inf
>>
>>>> Any idea about how to fix this? Thanks!
>>>> Yu Chuan
>>
>>>> --
>>>> 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
>>>> Groups "aroma.affymetrix" group.
>>>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>>>> To unsubscribe from this group, send email to
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>>>> For more options, visit this group
>>>> athttp://groups.google.com/group/aroma-affymetrix?hl=en
>>
>>> ------------------------------
>>> Mark Robinson, PhD (Melb)
>>> Epigenetics
>>
>> ...
>>
>> read more ยป
>
> --
> 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
> Groups "aroma.affymetrix" group.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe from this group, send email to
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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
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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