Re: [aroma.affymetrix] Re: QC analysis and HuEx
You're probably interested in http://aroma-project.org/chipTypes/HuEx-1_0-st-v2 /Henrik On Thu, Feb 27, 2014 at 3:24 PM, Saskia Freytag sas.frey...@gmail.com wrote: Hello, I have exactly the same problem. Unfortunately the link which fixed your problem seems to be broken. Can anyone point me to the right cdfs. Thank you in advance, Saskia Am Freitag, 26. Februar 2010 12:12:10 UTC+11 schrieb zaid: Today I tried the same files using an updated CDF file from this page: http://groups.google.com/group/aroma-affymetrix/web/affymetrix-defined-transcript-clusters and the NUSE and RLE plots worked fine. In my previous trials, I was trying an older version of the CDF files posted on the above page and converted binary cdf versions of affymetrix. I re-created the problem again here are the results. readUnits(csN,units=1:2) $`2'-PDE` $`2'-PDE`$`201626` $`2'-PDE`$`201626`$intensities [,1][,2][,3][,4][, 5][,6][,7] [1,] 30.173895 20.211313 25.557259 13.2232994.772590 34.572330 22.838047 [2,] 35.341541 30.020275 15.349304 18.235540 66.222588 94.837425 70.914474 [3,] 99.606659 154.452805 52.543839 72.683655 46.566010 164.298965 142.068192 [4,] 339.529724 390.837433 450.683594 342.991272 343.375885 503.298981 375.991272 [5,] 993.837463 1355.145142 955.837463 680.606689 947.145142 1065.529785 1042.760498 [6,] 2059.375977 1565.068237 1917.452759 1170.452881 1414.452881 1649.375854 1763.529785 [7,] 59.302147 25.7608644.419939 47.258316 36.228756 39.274750 51.620762 [8,] 41.764843 15.8540048.483532 30.558447 26.374550 70.529938 75.837463 [9,] 239.298965 414.452820 233.837418 319.914337 184.145111 455.222046 286.529724 [10,] 172.683578 184.683578 196.222046 331.606659 180.606659 308.683594 266.991272 [11,] 44.131218 10.264504 21.390810 99.606659 42.149456 96.606659 314.760498 [12,]2.5041683.9204663.1859017.7499983.508877 11.280955 39.556137 [13,]9.6504343.7984246.5668875.2296065.811605 54.001240 30.096972 [14,] 31.121769 19.502832 37.736290 107.145119 21.467726 92.991272 59.532917 [15,]2.9551772.2799273.1697602.9686214.713497 7.9560123.671075 [16,] 98.222038 68.530075 74.914391 73.068268 48.941250 41.226379 73.299034 [17,] 24.754116 39.120903 57.534470 48.325867 45.347137 24.984880 33.228832 [18,]4.2238905.2296065.301873 17.7857445.052575 7.8979753.898368 [19,]2.9686213.6200723.0199382.4756644.163679 3.1697603.975102 [20,] 79.837433 20.211313 16.544165 90.760506 21.951843 40.786907 86.837425 [21,] 25.326687 27.180756 30.967922 82.991272 32.921154 49.556633 81.068199 [22,]9.1675455.9608113.584546 102.298965 12.389921 27.334526 61.608761 [23,] 100.683578 95.068192 46.873703 178.452805 107.145119 69.837631 125.683578 [24,] 281.298950 197.145111 179.068192 503.298981 283.145111 377.606659 233.991272 [25,] 162.683578 35.110786 132.914352 455.298981 163.683578 398.298981 390.452820 [26,] 48.864326 33.998024 65.684128 386.375885 162.222046 192.068192 139.837418 [27,]9.004797 16.787853 24.984880 90.222038 15.030814 146.298965 106.375885 [28,] 36.536449 83.068199 47.873703 273.145111 26.528273 297.837433 10.586439 [29,] 402.991272 273.298950 435.760498 971.145142 486.298981 678.914368 529.760498 [30,] 288.068207 68.991478 370.837433 561.222046 269.068207 422.222046 174.529724 [31,] 150.222046 30.967922 211.145111 355.760498 159.222046 544.914368 171.068192 [32,] 94.145119 94.837425 80.068207 235.991272 101.222038 371.683594 168.529724 [33,] 96.683578 76.529755 80.991280 246.452805 114.375885 412.991272 287.914337 [34,] 155.606659 113.683578 134.991272 323.375885 217.298965 292.837433 200.991272 [35,] 34.726177 42.072533 64.376762 208.837418 77.760513 131.606659 182.145111 [36,] 94.145119 31.506207 31.813900 96.452812 42.303303 65.684128 37.680859 [37,] 33.2288324.7725902.993202 42.534073 42.977371 122.991272 33.844215 [38,] 34.138268 41.226379 30.635365 63.684872 49.708897 87.1451194.538531 [39,] 14.751531 41.918686 28.155693 100.837425 18.714483 104.298965 26.066858 [,8][,9] [,10] [,11] [, 12] [,13] [1,] 21.0096769.581000 24.0657026.891736 35.110786 98.452812 [2,] 43.208138 51.851532 33.844215 58.303699 38.043980 66.222588 [3,] 107.606659 46.270214 92.683578 71.376007 64.222916 87.606659 [4,] 682.529724 240.222046 362.298950 396.683594 442.606659 257.375885 [5,] 1949.145142 682.914368 1022.606689 1050.529785 949.222046
Re: [aroma.affymetrix] Re: QC analysis and HuEx
Ok, before we try to troubleshoot this one, please update to the latest aroma.affymetrix version. The one you are using is nearly three months old, and I prefer to troubleshoot the current code base. When you've done that, it should be enough to run plotRle(); you don't have to rerun everything. BTW, did you remember to call fit() on the probe-level model? /Henrik On Wed, Feb 24, 2010 at 8:15 PM, zaid z...@genomedx.com wrote: 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) qamTr QualityAssessmentModel: Name: tissues Tags: RBC,QN,RMA,merged,QC Path: qcData/tissues,RBC,QN,RMA,merged,QC/HuEx-1_0-st-v2 Chip-effect set: ExonChipEffectSet: Name: tissues Tags: RBC,QN,RMA,merged Path: plmData/tissues,RBC,QN,RMA,merged/HuEx-1_0-st-v2 Platform: Affymetrix Chip type: HuEx-1_0-st-v2,monocell Number of arrays: 2 Names: S370-A-HuEx-1_0-st-v2-01-1 (S09-13138), S371-A-HuEx-1_0-st- v2-01-1 (S09-07848) Time period: 2010-02-24 10:28:31 -- 2010-02-24 10:28:31 Total file size: 5.43MB RAM: 0.01MB Parameters: (probeModel: chr pm, mergeGroups: logi TRUE) RAM: 0.00MB sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=C LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.6.0 aroma.affymetrix_1.3.0 aroma.apd_0.1.7 affxparser_1.18.0 [5] R.huge_0.2.0 aroma.core_1.3.1 aroma.light_1.15.1 matrixStats_0.1.8 [9] R.rsp_0.3.6 R.filesets_0.6.5 digest_0.4.1 R.cache_0.2.0 [13] R.utils_1.2.4 R.oo_1.6.5 affy_1.24.2 R.methodsS3_1.0.3 loaded via a namespace (and not attached): [1] affyio_1.14.0 preprocessCore_1.8.0 How can i get more details on the error. I tried to use less CEL files and as few as 3, still no luck. Thanks in advance On Feb 24, 10:46 am, Henrik Bengtsson henrik.bengts...@gmail.com wrote: Hi, there are probably more output from the error, or ? If so, could you please provide us with that one? Also, whenever you get an error, is it is always helpful to report output of traceback() [see email footer]. What's your sessionInfo()? /Henrik On Wed, Feb 24, 2010 at 7:29 PM, zaid z...@genomedx.com wrote: Error: Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars $yaxs) : NAs not allowed in 'ylim' On Feb 24, 10:19 am, zaid z...@genomedx.com wrote: I was doing QC analysis in aroma in R on HuEx chip but got an error while trying to plot NUSE. ylim contains NA. I'm running R 2.10(32bit) on a windows 7(64bit). my command: library(aroma.affymetrix) verbose - Arguments$getVerbose(-8, timestamp=TRUE) chipType - HuEx-1_0-st-v2 cdf - AffymetrixCdfFile$byChipType(chipType) print(cdf) cs - AffymetrixCelSet$byName(tissues, cdf=cdf) bc - RmaBackgroundCorrection(cs) csBC - process(bc,verbose=verbose) qn - QuantileNormalization(csBC, typesToUpdate=pm) csN - process(qn, verbose=verbose) plmTr - ExonRmaPlm(csN, mergeGroups=TRUE) fit(plmTr, verbose=verbose) qamTr - QualityAssessmentModel(plmTr) plotNuse(qamTr) plotRle(qamTr) End of command I was able to run the previous on U95A data and Plus 2 data. Also, in the past I was able to run that on HuEx data. The cdf file I'm using is binary and used multiples ones (HuEx-1_0- st- v2,core,A20071112,EP.cdf, HuEx-1_0-st- v2,control,A20071112,EP.cdf, HuEx-1_0-st- v2,extended,A20071112,EP.cdf etc offered on Elizabeth's Columnhttp://groups.google.com/group/aroma-affymetrix/web/affymetrix-define... ) Could you please point me how to fix this problem? Thanks in advance -- 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 athttp://groups.google.com/group/aroma-affymetrix?hl=en- 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
[aroma.affymetrix] Re: QC analysis and HuEx
Updated all my packages: 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) sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=CLC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affyQCReport_1.24.0lattice_0.17-26 RColorBrewer_1.0-2 preprocessCore_1.8.0 [5] xtable_1.5-6 simpleaffy_2.22.0 gcrma_2.18.0 genefilter_1.28.1 [9] Biobase_2.6.0 aroma.affymetrix_1.4.0 aroma.apd_0.1.7affxparser_1.18.0 [13] R.huge_0.2.0 aroma.core_1.4.0 aroma.light_1.15.1 matrixStats_0.1.9 [17] R.rsp_0.3.6R.filesets_0.7.0 digest_0.4.2 R.cache_0.2.0 [21] R.utils_1.3.3 R.oo_1.6.7 affyPLM_1.22.0 affy_1.24.2 [25] R.methodsS3_1.1.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 Biostrings_2.14.8 [5] DBI_0.2-5 grid_2.10.0 IRanges_1.4.8 RSQLite_0.8-3 [9] splines_2.10.0 survival_2.35-7 tools_2.10.0 plotNuse(qamTr) Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars $yaxs) : NAs not allowed in 'ylim' plotRle(qamTr) Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars $yaxs) : NAs not allowed in 'ylim' cesTr - getChipEffectSet(plmTr) trFit - extractDataFrame(cesTr, units=1:3, addNames=TRUE) head(trFit) unitName groupName unit group cell S370-A-HuEx-1_0-st-v2-01-1 (S09-13138) 1 2315251 23152521 1 1 0 2 2315373 23153742 1 3 0 3 2315554 23155863 1 7 0 S371-A-HuEx-1_0-st-v2-01-1 (S09-07848) 1 0 2 0 3 0 Yes I have done fit() call using : fit(plmTr, verbose=verbose) Mark, I have tried 53 samples, 3 of the 53, 12 of the 53. A different set of CEL files of 13, 10 and 3. As well as different binary CDF files. I have created folders from scratch still no luck on HuEx, however u95A, and plus2 works with no problems. Thanks again for all the help. Would you like more information? Thanks in advance Zaid On Feb 24, 2:10 pm, Mark Robinson mrobin...@wehi.edu.au wrote: Hi Zaid. Another thing to check/report in your next update (after you update to the new aroma.affymetrix) is whether you have reasonable chip effects. This is what Henrik was eluding to in his last comment. bxp() which is eventually called by plotRle() will handle NAs, so that shouldn't be the problem. The thing it won't handle is if *all* values are NA or all equal to the same number e.g. 0. I seem to recall you had this issue before. For example, what does these commands give: [...all your previous stuff...] cesTr - getChipEffectSet(plmTr) trFit - extractDataFrame(cesTr, units=1:3, addNames=TRUE) head(trFit) One thing that worries/interests me is your comment I tried to use less CEL files and as few as 3. I've run plotRle() on 10s of samples and I suspect that is not the problem. Can you explain exactly what you tried? And, if not too much work, it may even be best to create a completely new directory as if you were starting from scratch (say, with a handful of files), run your entire script and report back. Cheers, Mark On 25-Feb-10, at 8:19 AM, Henrik Bengtsson wrote: Ok, before we try to troubleshoot this one, please update to the latest aroma.affymetrix version. The one you are using is nearly three months old, and I prefer to troubleshoot the current code base. When you've done that, it should be enough to run plotRle(); you don't have to rerun everything. BTW, did you remember to call fit() on the probe-level model? /Henrik On Wed, Feb 24, 2010 at 8:15 PM, zaid z...@genomedx.com wrote: 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) qamTr QualityAssessmentModel: Name: tissues Tags: RBC,QN,RMA,merged,QC Path:
