Hello,
I am using DEXseq for exon differential analysis. The analysis seems to work
well on genes with several exons, but I have a problem with genes with only
one exon.
Let me present you my dataset:
pData(ecs)
sizeFactor condition replicate type
Raman_1 0.9638822 nonvir 1 paired-end
HM1_1 1.4000715 vir 1 paired-end
Raman_2 1.0314049 nonvir 2 paired-end
Raman_3 1.0734133 nonvir 3 paired-end
HM1_2 0.7801269 vir 2 paired-end
HM1_3 0.9488409 vir 3 paired-end
table( table (geneIDs(ecs)))
1 2 3 4 5 6 7 8
3149 893 874 206 100 42 18 4
As you can see, I have 3149 genes (out of 5286) which have only 1 exon.
There are 9291 exons.
res1 <- DEUresultTable(ecs)
> summary(res1)
geneID exonID dispersion_CR_est
EHI_051420 : 8 E001 :5286 Min. :0.000e+00
EHI_070690 : 8 E002 :2137 1st Qu.:7.176e-03
EHI_169670 : 8 E003 :1244 Median :1.693e-02
EHI_175010+EHI_175000.1: 8 E004 : 370 Mean :5.546e-02
EHI_005010 : 7 E005 : 164 3rd Qu.:3.641e-02
EHI_042710 : 7 E006 : 64 Max. :1.300e+01
(Other) :9245 (Other): 26 NA's :3.153e+03
dispersion pvalue padjust
Min. :2.010e-02 Min. : 0.0000 Min. : 0.0000
1st Qu.:2.202e-02 1st Qu.: 0.1150 1st Qu.: 0.4597
Median :2.628e-02 Median : 0.4054 Median : 0.8086
Mean :3.229e+04 Mean : 0.4269 Mean : 0.6775
3rd Qu.:4.214e-02 3rd Qu.: 0.7133 3rd Qu.: 0.9510
Max. :1.000e+08 Max. : 1.0000 Max. : 1.0000
NA's :3153.0000 NA's :3153.0000
There are 3153 NA's values. When checking out what were those NA's values, I
realized that they were all the genes with only one exon (and only 4 more
genes in the other cases). I doubt that it is by chance... And they don't
have weird read counts. Check for example EHI_000010, EHI_000410,
EHI_000420, EHI_000430, EHI_000440:
geneCountTable(ecs)[1:21,]
Raman_1 HM1_1 Raman_2 Raman_3 HM1_2 HM1_3
EHI_000010 391 1364 464 449 457 560
EHI_000130 18806 8116 21890 24994 6509 14067
EHI_000240 24057 21825 15365 26903 21101 27841
EHI_000250 3374 2689 3938 4854 2310 3556
EHI_000290 458 3721 437 550 1716 1054
EHI_000410 896 1041 1086 978 905 745
EHI_000420 140 220 244 117 140 78
EHI_000430 583 2043 304 634 1398 1197
EHI_000440 3103 15309 5358 3619 9152 10392
EHI_000450 358 559 991 516 281 564
EHI_000460.1 357 118 449 425 43 746
EHI_000470.1 408 2657 297 397 946 909
EHI_000480 842 1702 858 778 841 847
EHI_000490 187 648 221 239 370 249
EHI_000500 329 506 454 402 244 555
EHI_000520 482 1615 883 440 925 751
EHI_000530 1794 1588 1751 1966 1099 1860
EHI_000540 2857 2504 3706 4152 1479 2547
EHI_000550 1967 3999 1241 1904 2505 2448
EHI_000560 152 434 239 165 273 175
EHI_000570 1209 2142 2183 1213 1905 2662
res1[1:20,]
geneID exonID dispersion_CR_est dispersion pvalue
EHI_000010:001 EHI_000010 E001 NA 0.02377712 NA
EHI_000130:001 EHI_000130 E001 0.074669451 0.07466945 0.48673539
EHI_000130:002 EHI_000130 E002 0.128972813 0.12897281 0.94279527
EHI_000130:003 EHI_000130 E003 0.019602219 0.02031871 0.84327914
EHI_000130:004 EHI_000130 E004 0.067337196 0.06733720 0.70429765
EHI_000240:001 EHI_000240 E001 0.043753997 0.04375400 0.74939865
EHI_000240:002 EHI_000240 E002 0.058562700 0.05856270 0.74939865
EHI_000250:001 EHI_000250 E001 0.031440630 0.03144063 0.70444841
EHI_000250:002 EHI_000250 E002 0.037457450 0.03745745 0.70444841
EHI_000290:001 EHI_000290 E001 0.021113888 0.02396819 0.05100089
EHI_000290:002 EHI_000290 E002 0.007626346 0.03471905 0.95676220
EHI_000290:003 EHI_000290 E003 0.036889359 0.03688936 0.03057067
EHI_000410:001 EHI_000410 E001 NA 0.02235347 NA
EHI_000420:001 EHI_000420 E001 NA 0.03395573 NA
EHI_000430:001 EHI_000430 E001 NA 0.02219522 NA
EHI_000440:001 EHI_000440 E001 NA 0.02037263 NA
EHI_000450:001 EHI_000450 E001 0.024495906 0.04492663 0.64717121
EHI_000450:002 EHI_000450 E002 0.020356260 0.02483641 0.64717121
EHI_000460.1:001 EHI_000460.1 E001 NA 0.02602179 NA
EHI_000470.1:001 EHI_000470.1 E001 NA 0.02254333 NA
padjust
EHI_000010:001 NA
EHI_000130:001 0.8639624
EHI_000130:002 0.9927663
EHI_000130:003 0.9756197
EHI_000130:004 0.9503086
EHI_000240:001 0.9611397
EHI_000240:002 0.9611397
EHI_000250:001 0.9503086
EHI_000250:002 0.9503086
EHI_000290:001 0.2890521
EHI_000290:002 0.9962043
EHI_000290:003 0.2087239
EHI_000410:001 NA
EHI_000420:001 NA
EHI_000430:001 NA
EHI_000440:001 NA
EHI_000450:001 0.9278993
EHI_000450:002 0.9278993
EHI_000460.1:001 NA
EHI_000470.1:001 NA
I checked the model in the documentation and I don't see why the test does
not give a result in this case. Has anyone get the same problem?
Thanks for your help,
Jane Merlevède
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