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 > Groups "aroma.affymetrix" group. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en ------------------------------ 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 To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en