Question: DEXSeq filtering
0
gravatar for mali salmon
7.4 years ago by
mali salmon330
Israel
mali salmon330 wrote:
Hello list Two questions regarding DEXseq 1. Would you recommend to do an independent filtering prior to differential exon expression analysis (similar to what is done with gene expression analysis)? 2. What about exons with 0 counts across all samples, does DEXSeq uses them when estimating overall gene expression? would you recommend to remove those before analysis? Thanks Mali [[alternative HTML version deleted]]
dexseq • 1.1k views
ADD COMMENTlink modified 7.4 years ago by Simon Anders3.6k • written 7.4 years ago by mali salmon330
Answer: DEXSeq filtering
0
gravatar for Simon Anders
7.4 years ago by
Simon Anders3.6k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.6k wrote:
Hi Mali On 2012-05-31 07:47, mali salmon wrote: > Two questions regarding DEXseq > 1. Would you recommend to do an independent filtering prior to differential > exon expression analysis (similar to what is done with gene expression > analysis)? Use the parameter 'minCount' in estimateDispersions for this. The default, 10, is probably reasonable, but maybe a bit on the low end. Every exon with less than 10 counts (summed across all sample) is omitted from the tests. > 2. What about exons with 0 counts across all samples, does DEXSeq uses them > when estimating overall gene expression? would you recommend to remove > those before analysis? No need to remove them manually, estimateDispersion does this anyway. Simon
ADD COMMENTlink written 7.4 years ago by Simon Anders3.6k
Thanks Simon for your helpful prompt answer Mali On Thu, May 31, 2012 at 9:35 AM, Simon Anders <anders@embl.de> wrote: > Hi Mali > > > On 2012-05-31 07:47, mali salmon wrote: > > Two questions regarding DEXseq >> 1. Would you recommend to do an independent filtering prior to >> differential >> exon expression analysis (similar to what is done with gene expression >> analysis)? >> > > Use the parameter 'minCount' in estimateDispersions for this. The default, > 10, is probably reasonable, but maybe a bit on the low end. Every exon with > less than 10 counts (summed across all sample) is omitted from the tests. > > > 2. What about exons with 0 counts across all samples, does DEXSeq uses >> them >> when estimating overall gene expression? would you recommend to remove >> those before analysis? >> > > No need to remove them manually, estimateDispersion does this anyway. > > Simon > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
ADD REPLYlink written 7.4 years ago by mali salmon330
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