[BioC] Beadarray SAMExample tutorial: readIllumina problem

[Sarah Allen]

Mike Smith <grimbough at ...> writes:

> 
> Hi Sarah,
> 
> Assuming you're using the latest version of beadarray (version >= 2.0.0),
> I'm afraid the information in the SAM Example work flow is rather outdated.
>  Many of the arguments to functions have changed and a better starting point
> for getting to grips with beadarray is to take a look at the vignette, which
> you can either download from here:
> http://bioconductor.org/help/bioc-views/2.7/bioc/html/beadarray.html or
> access via the command vignette("beadlevel").
> 
> The data itself is also quite outdated.  We haven't seen Illumina data with
> a .csv extension for a number of years, so beadarray by default looks for
> .txt files, which is something we may need to make more flexible.  You can
> download some more recent examples of data from here:
> http://www.compbio.group.cam.ac.uk/Resources/baloc/, although you'll need to
> BeadDataPackR package to extract the data.
> 
> I'll update our webpage to reflect the fact that the scripts are out of
> date, sorry that we haven't done that already.
> 
> I hope that's of some help,
> 
> 
Thanks very much for the advice. I had an inkling the manual was outdated wrt
the current version but I couldn't find anything more up-to-date on the
bioconductor site so I thought I'd try starting with that/it was as good a place
as any (I have no experience of either R or array analysis so I'm learning from
scratch!).

Thanks again, Sarah