Hi, Using the python scripts provided in DEXSeq package dexseq_prepare_annotation.py and dexseq_count.py) I obtained the ensemble.gff and exon counts per sample. Here's a table of the counts: case case case case control control control control control ENSG00000000003:001 135 173 248 262 193 213 132 207 156 ENSG00000000003:002 119 78 199 156 156 121 100 162 120 ENSG00000000003:003 90 83 156 95 109 128 62 127 111 ENSG00000000003:004 48 34 74 55 35 73 26 59 46 ENSG00000000003:005 24 13 30 33 23 35 23 27 26 ENSG00000000003:006 17 12 27 30 33 21 16 22 6 ENSG00000000003:007 51 43 83 65 77 76 21 91 51 Is there a way to import this table into DEXSeq and find the differentially expressed exons? Thank you very much. Regards, Nirmala [[alternative HTML version deleted]]

Dear Nirmala, You can use the function "read.HTSeqCounts" to import the output of the python scripts to an ExonCountSet object and run DEXSeq on it. You could check the pasilla vignette to see an example: http://bioconductor.jp/packages/2.9/data/experiment/vignettes/pasilla/ inst/doc/create_objects.pdf Best wishes, Alejandro > Hi, > > Using the python scripts provided in DEXSeq package dexseq_prepare_annotation.py and dexseq_count.py) I obtained the ensemble.gff and exon counts per sample. Here's a table of the counts: > > > case > > case > > case > > case > > control > > control > > control > > control > > control > > ENSG00000000003:001 > > 135 > > 173 > > 248 > > 262 > > 193 > > 213 > > 132 > > 207 > > 156 > > ENSG00000000003:002 > > 119 > > 78 > > 199 > > 156 > > 156 > > 121 > > 100 > > 162 > > 120 > > ENSG00000000003:003 > > 90 > > 83 > > 156 > > 95 > > 109 > > 128 > > 62 > > 127 > > 111 > > ENSG00000000003:004 > > 48 > > 34 > > 74 > > 55 > > 35 > > 73 > > 26 > > 59 > > 46 > > ENSG00000000003:005 > > 24 > > 13 > > 30 > > 33 > > 23 > > 35 > > 23 > > 27 > > 26 > > ENSG00000000003:006 > > 17 > > 12 > > 27 > > 30 > > 33 > > 21 > > 16 > > 22 > > 6 > > ENSG00000000003:007 > > 51 > > 43 > > 83 > > 65 > > 77 > > 76 > > 21 > > 91 > > 51 > > > > Is there a way to import this table into DEXSeq and find the differentially expressed exons? > > Thank you very much. > > Regards, > Nirmala > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]