Bioconductor Human Annotation Database Packages

Question

[koen.vdberge]

Dear all,

I am currently analyzing RNA-seq data regarding tumor types. I have found my DE genes through edgeR analysis. For annotation purposes I have used the "org.Hs.eg.db" Human genome database, version 2.10.1. We have mapped ENSEMBL gene IDs using the Bioconductor GOstats package, however we did not found matching genes for several of our ENSEMBL gene IDs. Therefore, I would like to ask whether there are any other preferred packages that are relatively up-to-date with which it would be possible to find more annotations.

Thank you in advance, Koen

Answer 1

[Sean Davis]

If you are using Ensembl annotations, consider using the biomaRt package.