Update makeGoSet doc

[lmsimp]

• Add a note about GO hierarchy
• Add a note/link about filterBinMSnSet
• In paper: @lmsimp to complete
• update TL vignette and load TL params rda file. Then remove then from andy2011.

Maybe also add a note in the vignette.

[lgatto]

@lmsimp - reminder about this issue: has these been done?

[lgatto]

There are major differences in the makeGoSet() example, that now returns only two GO terms. Not sure what happens. It might not be a problem, and just be the result of using old parameters to retrieve the terms, but I had to fix some examples. I am wondering if this GO functionality is still relevant and whether it could be deprecated. @lmsimp what do you think?

[lmsimp]

I haven't used this functionality in a while now. Initial thoughts are yes... I will take a look and confirm.
If we were to remove makeGoSet would this allow removal of biomaRt from dependencies?

[lgatto]

The whole vignette annotation stuff gets dropped (vignette 4), and part of the transfer learning (vignette 5). It would be quite radical.