That is great! Thank you for the quick response! 1.3.20 is not in biocLite yet and I cannot find an SVN repository to fetch it from. How can I obtain it? Stefan On Thu, Sep 20, 2012 at 12:20 PM, Alejandro Reyes <alejandro.reyes@embl.de>wrote: > Dear Stefan Dentro, > > Thank you very much for sending me your ExonCountSet object. It was a > small bug related to the order of your genes, since they are not grouped by > geneID in your ExonCountSet object. Could you please update to DEXSeq > 1.3.20? It is fixed there! > > Alejandro > > > Dear Stefano Dentro, >> >> Thanks for the information. It does not seem obvious to me to determine >> what is the problem. Would it be possible for you to send me your >> ExonCountSet object to give it a closer look? Of course, it would be >> treated with full confidentiality and deleted after detecting/solving >> the error. >> >> Alejandro Reyes >> >> >> Perhaps a clue: >>> >>> If I add a second gene to the small dataset I get the following error >>> message: >>> >>> genes >>>> >>> [1] "ENSG00000009780" "ENSG00000034533" >>> ... >>> >>>> cds = estimateDispersions(cds, minCount=2, maxExon=90) >>>> >>> Dispersion estimation. (Progress report: one dot per 100 genes) >>> Error in which(sapply(muhats, inherits, "try-error")) : >>> argument to 'which' is not logical >>> >>> >>> If I select two other genes, no error message, but one of the two >>> genes is still marked as not testable, whilst there is enough data: >>> >>>> genes >>>> >>> [1] "ENSG00000069345" "ENSG00000099889" >>> ... >>> >>>> fData(cds) >>>> >>> geneID exonID testable dispBeforeSharing dispFitted >>> dispersion pvalue padjust chr start end >>> >>> 3 ENSG00000069345 4 FALSE NA 0.03745547 >>> 0.03745547 NA NA 16 47001996 47002076 >>> 4 ENSG00000099889 16 TRUE 0.106713856 0.12728475 >>> 0.12728475 9.533455e-01 9.533455e-01 22 19960260 19960350 >>> 1381 ENSG00000099889 18 TRUE 0.039759265 0.11401613 >>> 0.11401613 8.020906e-05 3.809930e-04 22 19959409 19959494 >>> 1382 ENSG00000099889 15 TRUE 0.015147460 0.07255594 >>> 0.07255594 4.753684e-01 6.021333e-01 22 19960448 19960559 >>> 1383 ENSG00000099889 14 TRUE 0.020525216 0.05938316 >>> 0.05938316 5.829357e-03 1.107578e-02 22 19960642 19960840 >>> 1384 ENSG00000099889 13 TRUE 0.008016871 0.06746289 >>> 0.06746289 3.700721e-01 5.408746e-01 22 19961166 19961316 >>> 1385 ENSG00000099889 12 TRUE 0.030236839 0.07790661 >>> 0.07790661 1.964000e-01 3.109666e-01 22 19961635 19961762 >>> 1386 ENSG00000099889 9 TRUE 0.025364371 0.05520343 >>> 0.05520343 4.359563e-01 5.916549e-01 22 19964938 19965109 >>> 1387 ENSG00000099889 8 TRUE 0.064383214 0.07631387 >>> 0.07631387 2.412871e-09 2.292227e-08 22 19965481 19965598 >>> 6388 ENSG00000069345 8 FALSE NA 0.02990952 >>> 0.02990952 NA NA 16 46992915 46993042 >>> 6389 ENSG00000069345 7 FALSE NA 0.02943529 >>> 0.02943529 NA NA 16 46993187 46993331 >>> 6390 ENSG00000069345 6 FALSE NA 0.02756900 >>> 0.02756900 NA NA 16 46998523 46998719 >>> 6391 ENSG00000069345 5 FALSE NA 0.02919581 >>> 0.02919581 NA NA 16 47001425 47001558 >>> 6393 ENSG00000069345 3 FALSE NA 0.02784982 >>> 0.02784982 NA NA 16 47005261 47005484 >>> 6394 ENSG00000069345 2 FALSE NA 0.06403618 >>> 0.06403618 NA NA 16 47005808 47005867 >>> 23101 ENSG00000099889 11 TRUE 0.176647935 0.16264956 >>> 0.17664794 0.000000e+00 0.000000e+00 22 19963209 19963280 >>> 76702 ENSG00000099889 17 TRUE 0.042072149 0.55244196 >>> 0.55244196 8.569994e-07 5.427663e-06 22 19959881 19959934 >>> 79101 ENSG00000099889 2 FALSE NA 40.14086829 >>> 40.14086829 NA NA 22 19997978 19998031 >>> 79190 ENSG00000099889 19 TRUE 0.347541116 0.09043853 >>> 0.34754112 4.506187e-03 9.513061e-03 22 19958739 19958858 >>> 79566 ENSG00000069345 9 FALSE NA 0.02639237 >>> 0.02639237 NA NA 16 46989299 46991132 >>> 111562 ENSG00000099889 6 TRUE 0.036879156 0.03886331 >>> 0.03886331 2.370001e-04 6.432859e-04 22 19967266 19967765 >>> 122467 ENSG00000099889 5 TRUE 0.046550209 0.04180913 >>> 0.04655021 5.771771e-01 6.853978e-01 22 19968734 19969260 >>> 126533 ENSG00000099889 7 TRUE 0.023668263 0.05572503 >>> 0.05572503 1.439509e-04 5.470135e-04 22 19966420 19966603 >>> 127478 ENSG00000099889 10 TRUE 0.482851293 1.21253452 >>> 1.21253452 3.875210e-02 6.693545e-02 22 19964229 19964246 >>> 131502 ENSG00000099889 4 TRUE 0.064691260 0.07631174 >>> 0.07631174 2.174826e-04 6.432859e-04 22 19969456 19969614 >>> 135581 ENSG00000099889 20 TRUE 0.059913261 0.03024754 >>> 0.05991326 8.767254e-01 9.254324e-01 22 19957419 19958266 >>> 137473 ENSG00000099889 1 TRUE 0.623260704 0.39612292 >>> 0.62326070 8.554939e-01 9.254324e-01 22 20004112 20004331 >>> 147158 ENSG00000099889 3 TRUE 0.546816624 0.16681316 >>> 0.54681662 3.335978e-03 7.922947e-03 22 19978108 19978335 >>> 186433 ENSG00000069345 1 FALSE NA 0.03292932 >>> 0.03292932 NA NA 16 47007406 47007699 >>> strand transcripts log2fold(data/control) >>> 3 <na> <na> NA >>> 4 <na> <na> -0.03257363 >>> 1381 <na> <na> -0.99913247 >>> 1382 <na> <na> -0.16326931 >>> 1383 <na> <na> 0.46834227 >>> 1384 <na> <na> -0.19311802 >>> 1385 <na> <na> 0.24176762 >>> 1386 <na> <na> -0.14237513 >>> 1387 <na> <na> -1.20469634 >>> 6388 <na> <na> NA >>> 6389 <na> <na> NA >>> 6390 <na> <na> NA >>> 6391 <na> <na> NA >>> 6393 <na> <na> NA >>> 6394 <na> <na> NA >>> 23101 <na> <na> -2.68320588 >>> 76702 <na> <na> -2.91182540 >>> 79101 <na> <na> 21.32540529 >>> 79190 <na> <na> 1.08400450 >>> 79566 <na> <na> NA >>> 111562 <na> <na> 0.46147010 >>> 122467 <na> <na> 0.05583688 >>> 126533 <na> <na> 0.64272965 >>> 127478 <na> <na> -1.83381112 >>> 131502 <na> <na> 0.73838679 >>> 135581 <na> <na> -0.04311782 >>> 137473 <na> <na> 0.17841783 >>> 147158 <na> <na> 1.62180140 >>> 186433 <na> <na> NA >>> >>> counts(cds) >>>> >>> sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 >>> sample9 sample10 sample11 sample12 sample13 sample14 >>> 3 247 161 259 144 186 191 226 147 >>> 107 200 302 69 133 62 >>> 4 14 10 9 15 7 7 38 6 >>> 23 20 57 23 24 6 >>> 1381 24 42 23 8 24 15 41 14 >>> 18 22 102 15 40 5 >>> 1382 36 44 31 17 30 13 65 13 >>> 34 65 148 40 57 13 >>> 1383 29 40 33 5 25 37 73 13 >>> 53 115 296 46 93 19 >>> 1384 24 41 31 9 33 38 99 20 >>> 40 88 165 40 95 10 >>> 1385 9 31 29 21 20 9 61 7 >>> 42 63 132 48 77 10 >>> 1386 28 45 60 29 37 36 120 38 >>> 73 82 231 69 103 24 >>> 1387 15 81 42 6 43 43 122 30 >>> 32 51 91 34 38 6 >>> 6388 434 528 611 331 414 414 732 415 >>> 427 455 484 143 445 197 >>> 6389 505 828 1061 402 692 830 1096 633 >>> 396 472 583 174 415 200 >>> 6390 1008 1213 1696 991 959 1093 1533 884 >>> 1254 1325 3025 637 1164 672 >>> 6391 439 780 1151 437 692 612 1151 700 >>> 459 654 1134 241 435 222 >>> 6393 737 918 1301 683 786 940 1377 773 >>> 1069 1541 2603 613 1211 512 >>> 6394 49 64 145 32 106 99 159 64 >>> 47 35 41 15 46 6 >>> 23101 25 26 27 5 18 11 66 30 >>> 11 6 21 7 4 0 >>> 76702 6 10 5 0 6 1 19 9 >>> 2 0 3 2 4 0 >>> 79101 0 0 0 0 0 0 0 0 >>> 0 0 0 0 1 0 >>> 79190 23 1 8 0 9 1 62 5 >>> 44 46 160 31 41 15 >>> 79566 7133 6826 7143 6365 6600 6431 7394 4947 >>> 6323 7007 10031 1949 7597 4639 >>> 111562 50 96 65 51 107 50 184 47 >>> 136 365 675 174 235 69 >>> 122467 82 120 60 53 62 45 190 51 >>> 104 309 530 123 253 46 >>> 126533 24 49 28 19 19 21 73 22 >>> 88 131 221 96 101 25 >>> 127478 0 2 0 0 4 0 11 4 >>> 0 0 6 1 2 0 >>> 131502 24 24 22 12 6 3 60 3 >>> 33 84 208 48 85 15 >>> 135581 389 477 257 93 305 279 773 141 >>> 459 611 1830 361 766 173 >>> 137473 7 0 1 8 3 0 1 0 >>> 1 16 17 5 10 6 >>> 147158 5 3 4 0 3 6 10 0 >>> 0 52 27 8 23 21 >>> 186433 65 132 241 134 128 147 227 136 >>> 231 955 989 152 606 142 >>> sample15 sample16 sample17 sample18 sample19 sample20 sample21 >>> sample22 sample23 >>> 3 78 168 129 217 149 75 104 >>> 73 28 >>> 4 41 2 35 125 7 51 16 >>> 15 13 >>> 1381 14 4 27 82 4 61 20 >>> 34 7 >>> 1382 56 8 64 270 12 102 37 >>> 86 28 >>> 1383 68 25 103 393 20 159 55 >>> 105 51 >>> 1384 51 12 83 260 10 119 42 >>> 77 35 >>> 1385 40 19 82 222 7 115 41 >>> 54 17 >>> 1386 96 21 104 425 17 195 72 >>> 93 28 >>> 1387 28 11 40 163 9 88 30 >>> 63 16 >>> 6388 332 660 374 867 648 272 327 >>> 73 285 >>> 6389 253 556 353 785 471 268 292 >>> 152 205 >>> 6390 950 1687 1139 2477 1607 838 924 >>> 554 508 >>> 6391 337 646 437 1022 525 314 426 >>> 303 155 >>> 6393 815 1476 912 2385 1225 764 921 >>> 774 288 >>> 6394 15 21 28 16 10 21 11 >>> 14 8 >>> 23101 4 2 16 38 0 23 11 >>> 2 2 >>> 76702 1 0 1 6 0 3 2 >>> 2 3 >>> 79101 0 0 0 0 0 1 0 >>> 0 0 >>> 79190 26 6 85 79 8 133 37 >>> 71 29 >>> 79566 6589 10656 8383 11925 10680 3772 4360 >>> 2309 5646 >>> 111562 146 63 275 1046 42 423 186 >>> 330 56 >>> 122467 115 37 157 826 31 376 162 >>> 217 31 >>> 126533 85 19 97 421 26 215 99 >>> 98 31 >>> 127478 1 0 0 5 0 4 1 >>> 3 2 >>> 131502 35 21 56 266 13 136 56 >>> 60 16 >>> 135581 655 208 890 2407 176 953 358 >>> 577 413 >>> 137473 2 1 10 16 2 18 3 >>> 5 3 >>> 147158 14 1 16 97 8 98 17 >>> 18 6 >>> 186433 179 389 253 608 276 231 236 >>> 400 62 >>> >>> On Thu, Sep 20, 2012 at 9:31 AM, Stefan Dentro <sdentro@gmail.com>>> <mailto:sdentro@gmail.com>> wrote: >>> >>> Hi Alejandro, >>> >>> I just reran the code with only ENSG00000009780 in the dataset. >>> The odd thing is that this time it worked perfectly. >>> >>> Regards, >>> Stefan >>> >>> >>> ## Only ENSG00000009780 >>> >>> >counts(cds) >>> sample1 sample2 sample3 sample4 sample5 sample6 sample7 >>> sample8 sample9 sample10 sample11 sample12 sample13 sample14 >>> 1 11 8 4 7 3 1 8 >>> 3 1 1 0 3 4 1 >>> 1100 1 0 1 1 0 0 0 >>> 1 2 0 0 0 0 1 >>> 13665 91 145 86 47 169 36 231 >>> 136 78 64 130 55 66 27 >>> 13666 19 62 32 18 44 23 61 >>> 38 7 20 51 6 43 8 >>> 13670 77 139 73 66 78 30 168 >>> 88 75 85 186 79 86 58 >>> 22095 78 94 52 47 40 41 121 >>> 60 64 64 149 51 91 37 >>> 22096 36 61 50 63 67 10 129 >>> 69 90 79 287 66 97 29 >>> 108973 3 5 3 0 1 0 4 >>> 2 1 0 0 1 1 0 >>> 136687 2 12 5 0 19 0 34 >>> 10 5 28 31 6 27 5 >>> 138629 42 96 50 24 98 23 117 >>> 79 119 111 233 100 129 59 >>> sample15 sample16 sample17 sample18 sample19 sample20 >>> sample21 sample22 sample23 >>> 1 1 0 3 7 0 0 >>> 1 0 0 >>> 1100 1 0 0 3 1 0 >>> 0 0 0 >>> 13665 75 53 49 126 36 37 >>> 48 53 24 >>> 13666 15 19 11 26 7 15 >>> 11 5 7 >>> 13670 70 86 47 149 82 49 >>> 66 38 27 >>> 22095 67 54 58 148 54 41 >>> 64 43 25 >>> 22096 75 92 58 126 67 55 >>> 71 51 21 >>> 108973 1 1 0 4 0 0 >>> 0 0 1 >>> 136687 4 12 5 32 6 7 >>> 9 16 1 >>> 138629 141 103 70 219 92 60 >>> 74 67 54 >>> >>> >>> >fData(cds) >>> geneID exonID testable dispBeforeSharing >>> dispFitted dispersion pvalue padjust chr start end >>> 1 ENSG00000009780 4 TRUE 0.40135710 0.40580351 >>> 0.40580351 4.256220e-04 8.512441e-04 1 28059114 28059168 >>> 1100 ENSG00000009780 3 TRUE 0.57127358 1.98755125 >>> 1.98755125 9.715722e-01 9.715722e-01 1 28056743 28056844 >>> 13665 ENSG00000009780 9 TRUE 0.01991574 0.03806432 >>> 0.03806432 2.537419e-09 1.268709e-08 1 28086037 28086138 >>> 13666 ENSG00000009780 7 TRUE 0.09257216 0.07072531 >>> 0.09257216 6.740254e-07 2.246751e-06 1 28075579 28075665 >>> 13670 ENSG00000009780 6 TRUE 0.01517262 0.03752086 >>> 0.03752086 7.138709e-01 7.931899e-01 1 28071165 28071322 >>> 22095 ENSG00000009780 8 TRUE 0.03299040 0.04028325 >>> 0.04028325 5.589838e-01 6.987297e-01 1 28081706 28081841 >>> 22096 ENSG00000009780 5 TRUE 0.04659993 0.03930375 >>> 0.04659993 1.632722e-04 4.081804e-04 1 28060542 28060694 >>> 108973 ENSG00000009780 2 TRUE 0.01382188 0.99934256 >>> 0.99934256 6.159293e-02 1.026549e-01 1 28053983 28054047 >>> 136687 ENSG00000009780 1 TRUE 0.38138204 0.12609379 >>> 0.38138204 1.302911e-01 1.861302e-01 1 28052568 28052672 >>> 138629 ENSG00000009780 10 TRUE 0.01782266 0.03578012 >>> 0.03578012 7.407408e-12 7.407408e-11 1 28087006 28087092 >>> strand transcripts log2fold(data/control) >>> 1 <na> <na> -1.89528866 >>> 1100 <na> <na> -0.01821944 >>> 13665 <na> <na> -0.79494559 >>> 13666 <na> <na> -1.13738728 >>> 13670 <na> <na> -0.06639675 >>> 22095 <na> <na> 0.07349758 >>> 22096 <na> <na> 0.52608193 >>> 108973 <na> <na> -1.59373125 >>> 136687 <na> <na> 0.56880558 >>> 138629 <na> <na> 0.85158758 >>> >>> >>> >>> On Wed, Sep 19, 2012 at 5:20 PM, Alejandro Reyes >>> <alejandro.reyes@embl.de <mailto:alejandro.reyes@embl.**de<alejandro.reyes@embl.de="">>> >>> wrote: >>> >>> Dear Stefan Dentro, >>> >>> Thanks for your email. It actually looks strange, could you >>> send the output of the function "counts", and subset for this >>> specific gene? Could you also do it for the "fData" function?? >>> >>> Alejandro >>> >>> >>> Hello, >>> >>> I'm using DEXSeq to obtain differentially expressed exons >>> between my 15 >>> samples and 8 controls. But for some reason most exons are >>> not testable and >>> are not assigned a p-value. Do you know what I'm doing >>> wrong? >>> >>> First I've created a conservative list of exons per gene >>> in the human >>> genome through the canonical transcripts table in UCSC >>> (194511 in total). >>> Next I've obtained read counts for each exon in each >>> sample which are read >>> into one big data.frame. Then the following list of >>> commands are executed: >>> >>> metadata = data.frame( >>> row.names=colnames(dat)[7:29], >>> condition=c(rep("control", 8), rep("data", 15)), >>> replicate=c(c(1:8), c(1:15)), >>> libType=rep("paired-end", 23)) >>> >>> ## Add strand information that is not available in the >>> read counts >>> data.frame >>> dat = cbind(dat, strand=rep(NA, nrow(dat))) >>> >>> cds = newExonCountSet(countData = dat[,c(7:29)], design = >>> metadata, >>> geneIDs = dat[,5], exonIDs = >>> dat[,6], >>> exonIntervals=dat[,c(2,3,4, 30)]) >>> >>> cds = estimateSizeFactors(cds) >>> cds = estimateDispersions(cds, minCount=2, maxExon=90) >>> cds = fitDispersionFunction(cds) >>> cds = testForDEU(cds) >>> cds = estimatelog2FoldChanges(cds) >>> >>> Now lets see how many exons are expressed significantly >>> different between >>> data and controls. Surprisingly only 1850 exons are >>> described here, not the >>> full 194511: >>> >>> res1 = DEUresultTable(cds) >>> table(res1$padjust < 0.05) >>> >>> FALSE TRUE >>> 1424 426 >>> >>> So I've zoomed in to an example gene. Below it can be seen >>> that indeed all >>> exons are marked as not testable. But looking at the >>> individual read counts >>> per sample (see further below) it does not make sense that >>> they are not >>> testable. Some exons indeed have a low read count and are >>> excluded >>> rightfully, but others have enough reads to base >>> dispersion on I would >>> think. >>> >>> If I have understood correctly testable can be false in >>> either of these >>> cases: >>> - Gene has only one exon, dispersion cannot be calculated. >>> - Readcounts for an exon are too low. >>> - A combination of the above. >>> >>> But all do not apply here. Any ideas? >>> >>> >>> fData for the gene: >>> geneID exonID testable dispBeforeSharing >>> dispFitted >>> dispersion pvalue padjust chr start end strand >>> transcripts >>> 136687 ENSG00000009780 1 FALSE NA >>> 0.2026585 >>> 0.2026585 NA NA 1 28052568 28052672 <na> <na> >>> 108973 ENSG00000009780 2 FALSE NA >>> 0.9549670 >>> 0.9549670 NA NA 1 28053983 28054047 <na> <na> >>> 1100 ENSG00000009780 3 FALSE NA >>> 1.9560912 >>> 1.9560912 NA NA 1 28056743 28056844 <na> <na> >>> 1 ENSG00000009780 4 FALSE NA >>> 0.4722995 >>> 0.4722995 NA NA 1 28059114 28059168 <na> <na> >>> 22096 ENSG00000009780 5 FALSE NA >>> 0.1146813 >>> 0.1146813 NA NA 1 28060542 28060694 <na> <na> >>> 13670 ENSG00000009780 6 FALSE NA >>> 0.1127563 >>> 0.1127563 NA NA 1 28071165 28071322 <na> <na> >>> 13666 ENSG00000009780 7 FALSE NA >>> 0.1450013 >>> 0.1450013 NA NA 1 28075579 28075665 <na> <na> >>> 22095 ENSG00000009780 8 FALSE NA >>> 0.1160550 >>> 0.1160550 NA NA 1 28081706 28081841 <na> <na> >>> 13665 ENSG00000009780 9 FALSE NA >>> 0.1129432 >>> 0.1129432 NA NA 1 28086037 28086138 <na> <na> >>> 138629 ENSG00000009780 10 FALSE NA >>> 0.1112855 >>> 0.1112855 NA NA 1 28087006 28087092 <na> <na> >>> >>> Read counts for the gene per sample: >>> exon_id chr start end gene_id >>> exon_nr >>> sample1 sample2 sample3 sample4 sample5 sample6 sample7 >>> sample8 >>> 1 ENSE00000327880 1 28059114 28059168 >>> ENSG00000009780 4 >>> 11 8 4 7 3 1 8 3 >>> 1100 ENSE00000571221 1 28056743 28056844 >>> ENSG00000009780 3 >>> 1 0 1 1 0 0 0 1 >>> 13665 ENSE00000761751 1 28086037 28086138 >>> ENSG00000009780 9 91 >>> 145 86 47 169 36 231 136 >>> 13666 ENSE00000761753 1 28075579 28075665 >>> ENSG00000009780 7 19 >>> 62 32 18 44 23 61 38 >>> 13670 ENSE00000761780 1 28071165 28071322 >>> ENSG00000009780 6 77 >>> 139 73 66 78 30 168 88 >>> 22095 ENSE00000866714 1 28081706 28081841 >>> ENSG00000009780 8 78 >>> 94 52 47 40 41 121 60 >>> 22096 ENSE00000866716 1 28060542 28060694 >>> ENSG00000009780 5 36 >>> 61 50 63 67 10 129 69 >>> 108973 ENSE00001625313 1 28053983 28054047 >>> ENSG00000009780 2 >>> 3 5 3 0 1 0 4 2 >>> 136687 ENSE00001909353 1 28052568 28052672 >>> ENSG00000009780 1 2 >>> 12 5 0 19 0 34 10 >>> 138629 ENSE00001955917 1 28087006 28087092 >>> ENSG00000009780 10 >>> 42 96 50 24 98 23 117 79 >>> sample9 sample10 sample11 sample12 sample13 >>> sample14 sample15 >>> sample16 sample17 sample18 sample19 sample20 sample21 >>> sample22 >>> 1 1 1 0 3 4 1 1 >>> 0 3 7 0 0 1 0 >>> 1100 2 0 0 0 0 1 1 >>> 0 0 3 1 0 0 0 >>> 13665 78 64 130 55 66 27 75 >>> 53 49 126 36 37 48 53 >>> 13666 7 20 51 6 43 8 15 >>> 19 11 26 7 15 11 5 >>> 13670 75 85 186 79 86 58 70 >>> 86 47 149 82 49 66 38 >>> 22095 64 64 149 51 91 37 67 >>> 54 58 148 54 41 64 43 >>> 22096 90 79 287 66 97 29 75 >>> 92 58 126 67 55 71 51 >>> 108973 1 0 0 1 1 0 1 >>> 1 0 4 0 0 0 0 >>> 136687 5 28 31 6 27 5 4 >>> 12 5 32 6 7 9 16 >>> 138629 119 111 233 100 129 59 >>> 141 >>> 103 70 219 92 60 74 67 >>> sample23 strand >>> 1 0 NA >>> 1100 0 NA >>> 13665 24 NA >>> 13666 7 NA >>> 13670 27 NA >>> 22095 25 NA >>> 22096 21 NA >>> 108973 1 NA >>> 136687 1 NA >>> 138629 54 NA >>> >>> Design of the experiment: >>> condition replicate libType >>> sample1 control 1 paired-end >>> sample2 control 2 paired-end >>> sample3 control 3 paired-end >>> sample4 control 4 paired-end >>> sample5 control 5 paired-end >>> sample6 control 6 paired-end >>> sample7 control 7 paired-end >>> sample8 control 8 paired-end >>> sample9 data 1 paired-end >>> sample10 data 2 paired-end >>> sample11 data 3 paired-end >>> sample12 data 4 paired-end >>> sample13 data 5 paired-end >>> sample14 data 6 paired-end >>> sample15 data 7 paired-end >>> sample16 data 8 paired-end >>> sample17 data 9 paired-end >>> sample18 data 10 paired-end >>> sample19 data 11 paired-end >>> sample20 data 12 paired-end >>> sample21 data 13 paired-end >>> sample22 data 14 paired-end >>> sample23 data 15 paired-end >>> >>> sessionInfo() >>> >>> R version 2.15.0 (2012-03-30) >>> Platform: i686-pc-linux-gnu (32-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 >>> LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 >>> [6] LC_MESSAGES=C LC_PAPER=C LC_NAME=C >>> LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] plyr_1.7.1 DEXSeq_1.2.1 BiocInstaller_1.4.3 >>> DESeq_1.8.3 locfit_1.5-7 Biobase_2.16.0 >>> [7] BiocGenerics_0.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.34.0 AnnotationDbi_1.18.0 biomaRt_2.12.0 >>> DBI_0.2-5 genefilter_1.38.0 geneplotter_1.34.0 >>> [7] grid_2.15.0 hwriter_1.3 IRanges_1.14.2 >>> lattice_0.20-6 RColorBrewer_1.0-5 RCurl_1.91-1 >>> [13] RSQLite_0.11.1 splines_2.15.0 statmod_1.4.15 >>> stats4_2.15.0 stringr_0.6 survival_2.36-12 >>> [19] tools_2.15.0 XML_3.9-4 xtable_1.7-0 >>> >>> [[alternative HTML version deleted]] >>> >>> 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