[BioC] DEXSeq: Difference in splicing

Dario Beraldi Dario.Beraldi at cancer.org.uk
Thu Sep 27 17:42:29 CEST 2012

Great thanks! I don't know how I could have missed it... The name of the
function is quite self explanatory!
All the best


On 27/09/2012 16:27, "Alejandro Reyes" <alejandro.reyes at embl.de> wrote:

>Dear Dario,
>Please have a look into the function estimatelog2FoldChanges. With this
>you can get the log (base 2) fold changes!
>Best wishes,
>Alejandro Reyes
>> Hello,
>> I'm using DEXseq to detect differential splicing between two conditions
>>(3 replicates each) and following the guidelines in the vignettes I got
>>a nice table of differentially spliced exons (from DEUresultTable). So
>>far so good.
>> Now, in differential gene expression you quantify the difference as log
>>fold change between condition A and B. Likewise, I would like to
>>quantify the size of the difference in splicing and the direction. Is
>>this information available from DEXSeq?
>> Looking at the graph produced by plotDEXSeq() with splicing= TRUE it
>>seems to me that this information could come from the "fitted splicing"
>>(like FC= log2(fittedSplicingB/fittedSplicingA)).
>> However I can't find where the fitted splicing data is (I guess
>>somewhere in the ExonCountSet?)
>> By the way, I found this post
>>l asking a similar question and Wolfgang mentioned some improvements to
>>the output that could have been addressed in later releses of DEXSeq.
>> Many thanks!
>> Dario
>>   -- output of sessionInfo():
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> other attached packages:
>> [1] DEXSeq_1.2.1       Biobase_2.16.0     BiocGenerics_0.2.0
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.12.0 hwriter_1.3    plyr_1.7.1     RCurl_1.91-1
>> [6] stringr_0.6.1  tools_2.15.0   XML_3.9-4
>> --
>> Sent via the guest posting facility at bioconductor.org.
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