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 13.223299 4.772590 > 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 25.760864 4.419939 47.258316 36.228756 > 39.274750 51.620762 > [8,] 41.764843 15.854004 8.483532 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,] 2.504168 3.920466 3.185901 7.749998 3.508877 > 11.280955 39.556137 > [13,] 9.650434 3.798424 6.566887 5.229606 5.811605 > 54.001240 30.096972 > [14,] 31.121769 19.502832 37.736290 107.145119 21.467726 > 92.991272 59.532917 > [15,] 2.955177 2.279927 3.169760 2.968621 4.713497 > 7.956012 3.671075 > [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,] 4.223890 5.229606 5.301873 17.785744 5.052575 > 7.897975 3.898368 > [19,] 2.968621 3.620072 3.019938 2.475664 4.163679 > 3.169760 3.975102 > [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,] 9.167545 5.960811 3.584546 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,] 33.228832 4.772590 2.993202 42.534073 42.977371 > 122.991272 33.844215 > [38,] 34.138268 41.226379 30.635365 63.684872 49.708897 > 87.145119 4.538531 > [39,] 14.751531 41.918686 28.155693 100.837425 18.714483 > 104.298965 26.066858 > [,8] [,9] [,10] [,11] [, > 12] [,13] > [1,] 21.009676 9.581000 24.065702 6.891736 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 > 759.452820 > [6,] 2499.529785 1136.683594 1588.914307 1515.375854 1069.222046 > 1050.991333 > [7,] 56.919086 8.835921 14.464849 31.506207 12.584667 > 80.529739 > [8,] 21.951843 35.110786 25.557259 54.693550 52.389992 > 16.111414 > [9,] 142.683578 235.375885 502.452820 350.529724 255.837418 > 457.683594 > [10,] 17.643476 212.145111 197.683578 217.298965 222.068192 > 413.298950 > [11,] 9.167545 31.813900 78.683594 102.452812 35.495388 > 75.299004 > [12,] 3.881224 4.587281 6.431705 7.658939 6.566887 > 4.419939 > [13,] 5.229606 7.138066 26.066858 72.683655 23.788197 > 8.606457 > [14,] 5.229606 49.018173 36.074909 44.731750 36.151833 > 37.736290 > [15,] 3.019938 5.154222 3.105200 3.201177 3.756818 > 16.034637 > [16,] 95.914345 101.298965 72.376007 38.582443 65.222916 > 78.606667 > [17,] 42.072533 7.023152 20.211313 48.864326 22.914968 > 24.217855 > [18,] 3.855694 4.371360 9.427630 6.258907 5.052575 > 3.975102 > [19,] 4.275052 2.955177 4.419939 2.819058 3.473291 > 2.054114 > [20,] 2.899159 28.386461 16.863979 77.529755 95.760506 > 31.813900 > [21,] 3.550558 59.609840 32.198513 52.236149 73.529808 > 113.529732 > [22,] 4.188257 17.643476 12.721886 32.998077 46.193291 > 77.914360 > [23,] 5.545773 31.583130 38.428596 125.606651 145.606659 > 155.452805 > [24,] 65.069069 218.683578 224.991272 258.068207 289.683594 > 361.914337 > [25,] 6.713028 103.760498 126.837425 186.298965 178.914352 > 231.145111 > [26,] 3.005447 68.145454 33.690372 113.760498 128.222046 > 163.298965 > [27,] 5.229606 30.173895 30.967922 18.714483 43.208138 > 34.572330 > [28,] 4.962061 71.606781 36.536449 47.027550 38.197826 > 40.786907 > [29,] 172.529724 437.375885 448.606659 634.298950 320.298950 > 417.760498 > [30,] 408.991272 275.222046 225.145111 435.529724 382.298950 > 249.068192 > [31,] 248.452805 282.222046 94.222038 206.145111 172.914352 > 123.760498 > [32,] 30.967922 81.914352 108.760498 136.760498 68.837746 > 232.914352 > [33,] 20.211313 85.760506 84.222046 161.298965 93.837425 > 196.298965 > [34,] 117.452805 248.683578 170.222046 182.760498 202.606659 > 71.529854 > [35,] 48.864326 84.529739 123.914345 52.466915 71.529854 > 165.222046 > [36,] 15.272806 33.613449 58.840611 57.457546 54.770473 > 127.760498 > [37,] 16.544165 20.029972 67.376228 55.459740 39.274750 > 45.962521 > [38,] 28.386461 92.683578 36.844131 37.074902 58.457279 > 115.452812 > [39,] 34.572330 37.680859 70.376091 45.962521 15.564535 > 17.567133 > > $`3.8-1` > $`3.8-1`$`352961` > $`3.8-1`$`352961`$intensities > [,1] [,2] [,3] [,4] [,5] [,6] [, > 7] [,8] [,9] > [1,] 67.68391 8.606457 4.142926 129.3759 44.43891 10.1953 > 113.6836 4.828296 10.07789 > [2,] 292.29895 111.760498 107.991272 203.9913 163.52972 199.1451 > 142.6836 21.009676 86.06820 > [,10] [,11] [,12] [,13] > [1,] 14.54105 29.11857 34.34156 16.32873 > [2,] 324.83743 127.29897 164.29897 46.71986 > > > > head(trFit) > unitName groupName unit group cell S359-A-HuEx-1_0-st- > v2-01-1(S06-19542) > 1 2'-PDE 201626 1 1 > 1 0 > 2 3.8-1 352961 2 1 > 2 0 > 3 3.8-1.3 353008 3 1 > 3 0 > S360-A-HuEx-1_0-st-v2-01-1(S06-16651) S361-A-HuEx-1_0-st- > v2-01-1(S08-7727) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > S362-A-HuEx-1_0-st-v2-01-1(S07-25350) S363-A-HuEx-1_0-st- > v2-01-1(S08-6195) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > S364-A-HuEx-1_0-st-v2-01-1(S07-356) S365-A-HuEx-1_0-st- > v2-01-1(S07-658) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > S366-A-HuEx-1_0-st-v2-01-1(06-25583) S367-A-HuEx-1_0-st- > v2-01-1(S07-12679) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > S368-A-HuEx-1_0-st-v2-01-1(S09-12818) S369-A-HuEx-1_0-st- > v2-01-1(S09-12851) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > S370-A-HuEx-1_0-st-v2-01-1(S09-13138) S371-A-HuEx-1_0-st- > v2-01-1(S09-07848) > 1 > 0 0 > 2 > 0 0 > 3 > 0 0 > > > In regards to the other question > > I was using seprate directories in the rawData (tissues, mydata) and > also I was using two different root directories as well (aroma and > aromaData). I didn't use the extract() function. > > No warnings or strange errors appeared. > > Thanks again > > On Feb 25, 12:03 pm, "Mark Robinson" <mrobin...@wehi.edu.au> wrote: > > Hi Zaid. > > > > So, its looks like your boxplot problem is easily explainable. ALL of > > your chip effects are 0. That'll lead to a fairly uninteresting RLE or > > NUSE plot. Let's try and figure out why. > > > > I assume you've done something like: > > > > [...] > > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) > > fit(plmTr, verbose=verbose) > > > > A couple things to check are: > > > > 1. Does your AffymetrixCelSet object 'csN' have reasonable data? Try ... > > > > readUnits(csN, units=1:2) > > > > 2. If that looks fine, how about we re-fit the probe level models, just > in > > case it got interrupted for whatever reason. Try ... > > > > fit(plmTr, verbose=verbose, force=TRUE) > > > > ... and then check whether the chip effects are non-zero, as before ... > > > > cesTr <- getChipEffectSet(plmTr) > > trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE) > > head(trFit) > > > > Report back on that when you get a chance. > > > > Also, you said: > > > > > 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. > > > > But you didn't tell us exactly what you've done. Did you use separate > > directories or did you use extract()? > > > > Is there anything else that you saw while the data was processing that is > > worth mentioning? Any strange errors/warnings? Did you accurately > create > > a custom CDF? > > > > Cheers, > > Mark > > > > > > > > > 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=C LC_TIME=English_Canada.1252 > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods > > > base > > > > > other attached packages: > > > [1] affyQCReport_1.24.0 lattice_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_0.1.7 affxparser_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_0.3.6 R.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 2315252 1 1 > > > 1 0 > > > 2 2315373 2315374 2 1 > > > 3 0 > > > 3 2315554 2315586 3 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: 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 <- > > > > ... > > > > 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. 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