Entering edit mode
5.5 years ago
catscampos
•
0
Hello everyone I'm new at EdgeR and annotation. I'm trying to do annotation through Ensembl biomart of the DGEs that I've obtained with EdgeR. I'm working with Triticum aestivum. I've calculated the DGEs:
Test for differential expression
fit <- lmFit(v,design)
fit <- eBayes(fit)
results <- decideTests(fit)
summary(results)
Int UndisvsDis OrnvsLol
Down 47457 1989 68
NotSig 19407 102663 107809
Up 41027 3239 14
topTable(fit,coef=3,sort.by="p")
Then annotation from Ensembl plants
ensembl_wheat = useMart(host="plants.ensembl.org", "plants_mart",
dataset = "taestivum_eg_gene")
ensembl_df <- getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","ensembl_peptide_id","external_gene_name","go_id","name_1006","definition_1006","namespace_1003","kegg_enzyme","embl"),mart=ensembl_wheat)
How can I proceed from here?
Thanks a lot! Catarina