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 »- Hide quoted text -
>
> - Show quoted text -
--
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