Packages for annotations

[TomSmithCGAT]

'Annotation and Visualisation of Differential Expression Results' explains there are multiple ways to obtain annotations and then demonstrates how to do this with AnnotationHub, which seems perfectly reasonable.

Bulk_RNAseq_Course_Base/Markdowns/11_Annotation_and_Visualisation.Rmd

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	Today we will use the `AnnotationHub` method. A workflow for annotation with
	biomaRt is included in the extended materials section accessible on the course
	website.

However, after this, we then load a set of annotations that was obtained via biomaRt. I assume this is a legacy issue. This is a bit confusing and I would suggest the loaded annotations should be obtained with AnnotationHub too.

Bulk_RNAseq_Course_Base/Markdowns/11_Annotation_and_Visualisation.Rmd

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	## One we prepared earlier and one-to-many relationships
	To ensure everyone is working with same annotation, we have created an annotation table.
	In this case we used the `biomaRt` package to download annotations directly from
	Ensembl. In this cases we can get additional columns, but will also sometimes get
	one-to-many relationships, where one Ensembl ID maps to multiple Entrez IDs. This
	sort of problem is common when mapping between annotation sources, but they have
	already been dealt with for us in AnnotationHub. If we wanted more control over
	this we would need to manually curate these one-to-many relationships ourselves.
	In annotation table below we have modified the column names and dealt with the
	one-to-many/missing issues for Entrez IDs. The code we used for doing this is
	available in the [extended materials section](S6_Annotation_With_BioMart.html).
	We will load out pre-created annotation table, and then combine it with our
	results table.
	```{r addAnnotation, message=FALSE}
	ensemblAnnot <- readRDS("RObjects/Ensembl_annotations.rds")

[AshKernow]

Yes, we should look at resolving this discrepancy. We no longer need the Chr, Start etc columns, just Symbol and Entrez.