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Old 06-25-2013, 11:32 AM   #1
marianaboroni
Junior Member
 
Location: BH- Brasil

Join Date: Feb 2011
Posts: 5
Default DEXSeq output

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:

Quote:
> 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

OUTPUT DESeq:

Quote:
> 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
How can I get the baseMeanA baseMeanB values using the DEXSeq package?

Thanks!

[]s

Mariana
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Old 06-26-2013, 12:09 AM   #2
areyes
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Location: Heidelberg

Join Date: Aug 2010
Posts: 165
Default

Hi Mariana,

If you are interested in the exon expression, you could just calculate the mean accross the raw counts. If you are interested in the fitted splicing coefficients (what is plotted in plotDEXSeq) you could have a look at the function estimatelog2FoldChanges to get this coefficients, especifically you have to set the parameter getOnlyEffects=TRUE.

Alejandro
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Old 02-17-2014, 08:35 AM   #3
zorin
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Location: Austria

Join Date: Feb 2014
Posts: 2
Default DEXseq meanBaseA meanBaseB

Could you please post some sample code how to extract the relevant coefficients in order to obtain proper meanBaseA / meanBaseB values in the DEUresultTable.
I'm new to DEXseq and would highly appreciate your input.
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