Hello! Just a quick question regarding DEXSeq: I have more variables in my experiment (9 samples), i.e. 3 different celltypes (variable of interest) taken from 4 different patients. To take into account when samples come from the same patient I included an additional factor to the sampleData table. I understand that I have to use the following formulae when it comes to testing for differential exon usage: formulaFullModel = ~ sample + exon + patient:exon + celltype:exon formulaReducedModel = ~ sample + exon + patient:exon And I assume (but it's not quite clear to me from reading the vignette) that I also have to add the additional patient variable to the design already when creating the DEXSeqDataSetFromHTSeq: dxd = DEXSeqDataSetFromHTSeq( countFiles, sampleData=sampleTable, design= ~ sample + exon + patient:exon + celltype:exon, flattenedfile=flattenedFile) Is this correct? Best, Simone

Hi Simone, Yes, this is correct. And then you pass the reduced model to testForDEU. I will double check the documentation and make sure its clearer. Bests, Alejandro Reyes > Hello! > > Just a quick question regarding DEXSeq: > > I have more variables in my experiment (9 samples), i.e. 3 different > celltypes (variable of interest) taken from 4 different patients. To > take into account when samples come from the same patient I included > an additional factor to the sampleData table. > > I understand that I have to use the following formulae when it comes > to testing for differential exon usage: > > formulaFullModel = ~ sample + exon + patient:exon + celltype:exon > formulaReducedModel = ~ sample + exon + patient:exon > > And I assume (but it's not quite clear to me from reading the > vignette) that I also have to add the additional patient variable to > the design already when creating the DEXSeqDataSetFromHTSeq: > > dxd = DEXSeqDataSetFromHTSeq( > countFiles, > sampleData=sampleTable, > design= ~ sample + exon + patient:exon + celltype:exon, > flattenedfile=flattenedFile) > > Is this correct? > > Best, > Simone > > _______________________________________________ > 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