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 13.223299 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
