[BioC] Annotation different expressed exon. results from DESeq

[Fabrice Tourre]

Alejandro,

Thank you. It is from DESeq. I have added GeneSymbol to the last
column. Here how should I understand ENSMUSG00000026727:016,
ENSMUSG00000026727:004，does it mean there are two exon 016 and 004 in
gene ENSMUSG00000026727 are different expressed in tow conditions?

id baseMean  baseMeanA    baseMeanB
1 ENSMUSG00000022150+ENSMUSG00000079102:009 851.0096 1697.09604    4.9231156
2                    ENSMUSG00000026727:016 239.6701  478.35562    0.9846231
3                    ENSMUSG00000026727:004 155.8972  311.79442    0.0000000
4 ENSMUSG00000022150+ENSMUSG00000079102:015 698.9853 1348.73940   49.2311562
5                    ENSMUSG00000025730:010 703.3964   56.87455 1349.9183017
6                    ENSMUSG00000005836:007 302.9137  590.07349   15.7539700

    foldChange log2FoldChange         pval         padj GeneSymbol
1  0.002900906      -8.429281 3.160644e-18 3.750609e-13       Dab2
2  0.002058350      -8.924296 1.458392e-12 8.653076e-08       Rsu1
3  0.000000000           -Inf 2.943669e-11 1.164378e-06       Rsu1
4  0.036501607      -4.775896 1.217087e-09 3.610671e-05       Dab2
5 23.735013823       4.568945 4.029933e-09 9.564321e-05     Rab40c
6  0.026698319      -5.227107 6.754638e-09 1.335910e-04      Gata6

On Mon, Mar 3, 2014 at 3:35 AM, Alejandro Reyes <alejandro.reyes at embl.de> wrote:
> Dear Fabrice,
>
> I think you meant DEXSeq.
> To classify events into alternative splicing types it is useful to go back
> to the alignment files and visualize the exon-exon junction reads, then it
> becomes obvious which are the events that are giving rise to the differences
> in exon usage.
>
> Best regards,
> Alejandro
>
>
>
>> Dear list,
>>
>> When I use DESeq find different expressed exon in tow conditions. e.g,
>>
>>     id baseMean  baseMeanA    baseMeanB
>> 1 ENSMUSG00000079102:009 851.0096 1697.09604    4.9231156
>> 2 ENSMUSG00000026727:016 239.6701  478.35562    0.9846231
>> 3 ENSMUSG00000026727:004 155.8972  311.79442    0.0000000
>>
>> How can know the Alternative Splicing Event for
>> ENSMUSG00000079102:009, ENSMUSG00000026727:016 and
>> ENSMUSG00000026727:004?
>> for example, Cassette exon (skipped exon), Intron retention, Mutually
>> exclusive exons, Alternative 3' sites, Alternative 5' sites,
>> Alternative first exon.
>>
>> Thank you very much in advance.
>>
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>