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-analysis ---------------- 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 > 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
