[BioC] AnnBuilder problem with custom List of genes

[Marc Carlson]

claudio.is at libero.it wrote:
> this is the top of my input file
>
> "A25"   "AA415819"
> "A26"   "AA474746"
> "A27"   "AA473306"
> "A28"   "AA545607"
> "A29"   "AA413090"
> "A30"   "AA386616"
> "A31"   "AA437482"
> "A32"   "AA412921"
> "A33"   "AI508650"
> "A34"   "AA386794"
>
> is it correct?
>
>
> ---------- Initial Header -----------
>
> >From      : "Marc Carlson" mcarlson at fhcrc.org
> To          : "claudio.is at libero.it" claudio.is at libero.it
> Cc          : "jzhang" jzhang at jimmy.harvard.edu,"bioconductor" bioconductor at stat.math.ethz.ch
> Date      : Thu, 16 Aug 2007 15:02:03 -0700
> Subject : Re: [BioC] AnnBuilder problem with custom List of genes
>
>
>
>   

Nope.  You don't want the quotes, and this file needs to be strictly tab
delimited (not spaces).  When I run your IDs as you have them listed
here, I reproduce your bug and get empty fields.  But when I clean them
up so that they match the reccomendations in the AnnBuilder vignette
(ie. just plain strings separated by tabs), then they work just fine.

You might also find the following helpful:
http://www.bioconductor.org/repository/devel/vignette/AnnBuilder.pdf

Good luck with your project,

    Marc