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Question: DEXSeq: Difference in splicing
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4.6 years ago by
Guest User12k
Guest User12k 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: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 statmod_1.4.15 [6] stringr_0.6.1 tools_2.15.0 XML_3.9-4 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.6 years ago by Alejandro Reyes1.4k • written 4.6 years ago by Guest User12k
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4.6 years ago by
Alejandro Reyes1.4k
Germany
Alejandro Reyes1.4k 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 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: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 statmod_1.4.15 > [6] stringr_0.6.1 tools_2.15.0 XML_3.9-4 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 4.6 years ago by Alejandro Reyes1.4k
Great thanks! I don't know how I could have missed it... The name of the function is quite self explanatory! All the best Dario 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 >>https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-August/002167.htm >>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 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 >>statmod_1.4.15 >> [6] stringr_0.6.1 tools_2.15.0 XML_3.9-4 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:17}}
ADD REPLYlink written 4.6 years ago by Dario Beraldi10
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