Hi!
I've used the DESeq package and now I'm trying the DEXSeq one.
In the DESeq package I can access the baseMean, baseMeanA, baseMeanB values after doing the analysis as a output result, but using the DEXSeq package, I only get the meanBase value.
OUTPUT DEXSeq:
OUTPUT DESeq:
How can I get the baseMeanA baseMeanB values using the DEXSeq package?
Thanks!
[]s
Mariana
I've used the DESeq package and now I'm trying the DEXSeq one.
In the DESeq package I can access the baseMean, baseMeanA, baseMeanB values after doing the analysis as a output result, but using the DEXSeq package, I only get the meanBase value.
OUTPUT DEXSeq:
> res1 <- DEUresultTable(ecs)
> head(res1)
geneID exonID dispersion pvalue padjust meanBase log2fold(all/sl)
Smp_156060:E015 Smp_156060 E015 0.65669650 4.329870e-15 6.934596e-12 19.147740 -2.023423
Smp_141410:E001 Smp_141410 E001 0.48777320 2.455751e-06 7.733547e-04 7.941987 -1.977033
Smp_080520:E001 Smp_080520 E001 0.08365269 1.022540e-08 5.789747e-06 13.344642 -1.944765
Smp_194240:E001 Smp_194240 E001 0.33620393 4.173149e-06 1.285307e-03 2.973169 -1.930388
Smp_034190:E001 Smp_034190 E001 0.04309263 0.000000e+00 0.000000e+00 30.344916 -1.691994
Smp_091390:E001 Smp_091390 E001 0.07264235 0.000000e+00 0.000000e+00 15.738090 -1.682837
> head(res1)
geneID exonID dispersion pvalue padjust meanBase log2fold(all/sl)
Smp_156060:E015 Smp_156060 E015 0.65669650 4.329870e-15 6.934596e-12 19.147740 -2.023423
Smp_141410:E001 Smp_141410 E001 0.48777320 2.455751e-06 7.733547e-04 7.941987 -1.977033
Smp_080520:E001 Smp_080520 E001 0.08365269 1.022540e-08 5.789747e-06 13.344642 -1.944765
Smp_194240:E001 Smp_194240 E001 0.33620393 4.173149e-06 1.285307e-03 2.973169 -1.930388
Smp_034190:E001 Smp_034190 E001 0.04309263 0.000000e+00 0.000000e+00 30.344916 -1.691994
Smp_091390:E001 Smp_091390 E001 0.07264235 0.000000e+00 0.000000e+00 15.738090 -1.682837
OUTPUT DESeq:
> res1 <- nbinomTest( cds, "sl", "all" )
> head(res1)
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
1 Schisto_mansoni.mitochondria_rRNA1 1.081107e+04 2.668263 24321.567008 9115.130 13.15405 8.314941e-11 7.132301e-09
2 Schisto_mansoni.mitochondria_rRNA2 7.196552e+03 1.820197 16189.965875 8894.625 13.11872 7.980118e-06 5.303116e-05
3 Sm_mito_tRNA10.1 2.092785e+00 0.000000 4.708767 Inf Inf 3.392875e-01 5.555647e-01
4 Sm_mito_tRNA11.1 7.391640e-01 0.000000 1.663119 Inf Inf 8.837895e-01 1.000000e+00
5 Sm_mito_tRNA12.1 6.149918e-01 0.000000 1.383732 Inf Inf 1.000000e+00 1.000000e+00
6 Sm_mito_tRNA13.1 9.076016e-01 0.000000 2.042104 Inf Inf 8.429498e-01 1.000000e+00
> head(res1)
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
1 Schisto_mansoni.mitochondria_rRNA1 1.081107e+04 2.668263 24321.567008 9115.130 13.15405 8.314941e-11 7.132301e-09
2 Schisto_mansoni.mitochondria_rRNA2 7.196552e+03 1.820197 16189.965875 8894.625 13.11872 7.980118e-06 5.303116e-05
3 Sm_mito_tRNA10.1 2.092785e+00 0.000000 4.708767 Inf Inf 3.392875e-01 5.555647e-01
4 Sm_mito_tRNA11.1 7.391640e-01 0.000000 1.663119 Inf Inf 8.837895e-01 1.000000e+00
5 Sm_mito_tRNA12.1 6.149918e-01 0.000000 1.383732 Inf Inf 1.000000e+00 1.000000e+00
6 Sm_mito_tRNA13.1 9.076016e-01 0.000000 2.042104 Inf Inf 8.429498e-01 1.000000e+00
Thanks!
[]s
Mariana
Comment