Hello,
I am using DEXseq for differential analysis. I have posted some e-mails
about it already on this list, but I have more questions !
My dataset has 2 conditions with 3 biological replicates per condition:
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
I found the number of differentially expressed exons. I would like to know
also which are down and which are up regulated. This information is given by
foldChange, which is not provided in DEXSeq (res1).
res1 <- DEUresultTable(ecs)
head(res1)
geneID exonID dispersion_CR_est dispersion pvalue
EHI_000010:001 EHI_000010 E001 NA 0.02377712 NA
EHI_000130:001 EHI_000130 E001 0.07466945 0.07466945 0.4867354
EHI_000130:002 EHI_000130 E002 0.12897281 0.12897281 0.9427953
EHI_000130:003 EHI_000130 E003 0.01960222 0.02031871 0.8432791
EHI_000130:004 EHI_000130 E004 0.06733720 0.06733720 0.7042977
EHI_000240:001 EHI_000240 E001 0.04375400 0.04375400 0.7493987
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
So I would like to know, if it could be possible to have baseMean,
baseMeanA, baseMeanB, foldChange, log2FoldCHange, resVarA and resVarB as in
DESeq?
Since this does not seem to be implemented in DEXSeq, I should start with
the read counts per exon table to get it, but I can't find it neither. I
think it is use in the estimateSizeFactors function, but I don't manage to
access it. It's a pity, I will have to reconstruct the table...
Thank you for your help,
Jane Merlevède
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