Annotation from Ensembl plants to DGEs
0
0
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

RNA-Seq • 946 views
ADD COMMENT

Login before adding your answer.

Traffic: 2605 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6