Question: DEXSeq: Difference in splicing
5.1 years ago by
Guest User • 12k
Guest User • 12k wrote:
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 https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-August/002167.html 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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached):  biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 RCurl_1.91-1 statmod_1.4.15  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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