[BioC] beadarray package: problem with object made by createBeadSummaryData

[Martin Morgan]

Krys, Matt --

Since 1.7.2 is meant to work with the development version of R, using
1.7.2 implies that you really want to first move on to the 'bleeding
edge' by installing the development version of R (visit your local
CRAN, e.g., http://cran.fhcrc.org, then 'R binaries', then platform,
then look around a little (e.g., for Windows, click on 'base' and then
'r-devel snapshot build').

beadarray 1.7.2 is available via SVN, but also (typically 24-48 hours
after a patch) via biocLite -- biocLite retrieves the correct version
of the package for your version of R. On Windows and Mac this saves
you from having to install development tools.

You'll run into much less grief (and avoid the dreaded email exchange
'what is your sessionInfo()?' followed several hours later by 'update
your packages') by using only packages meant to work together with the
appropriate version of R.

Martin


Matt Ritchie <Matt.Ritchie at cancer.org.uk> writes:

> Hi Krys,
>
> You can checkout beadarray 1.7.2 from the BioC developmental svn repository
> (see http://wiki.fhcrc.org/bioc/SvnHowTo for instructions) and install it
> from source, or use the older version for R 2.5.1 - up to you!
>
> Best wishes,
>
> Matt
>
>> Hi Matt
>> 
>> So should I revert to R 2.5.1 or is there a way to access beadarray 1.7.2?
>> 
>> Thanks
>> 
>> Krys
>> 
>> 
>> -----Original Message-----
>> From: Matt Ritchie [mailto:Matt.Ritchie at cancer.org.uk]
>> Sent: 12 November 2007 19:01
>> To: Krys Kelly; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] beadarray package: problem with object made by
>> createBeadSummaryData
>> 
>> Hi Krys,
>> 
>> This is a bug, which has been fixed in beadarray 1.7.2.  Thanks for pointing
>> it out!  Best wishes,
>> 
>> Matt
>> 
>>> Hello
>>> 
>>> Using R 2.5.1, I have read in and explored the bead level data from 5
>>> Illumina mouse-6 slides which have 6 arrays per slide and 2 images per
>>> array.
>>> 
>>> I have also created and saved bead summary data trying out a few options
>> for
>>> the background correction.
>>> 
>>> When I was using R 2.5.1 and the corresponding versions of bioconductor
>> and
>>> beadarray and everything worked fine.
>>> 
>>> But I want to upgrade to R 2.6.0. I have installed R 2.6.0 and the
>>> corresponding versions of bioconductor and beadarray.  I now find that
>>> se.exprs is completely filled with NAs.
>>> 
>>> I have compared the documentation from the two versions of beadarray
>>> expecting that there was a new option that I needed to specify, but I
>> can't
>>> find anything that would account for the NAs
>>> 
>>> Please can you suggest what the problem is.
>>> 
>>> My program code, output from the BSData object and sessionInfo() are
>> pasted
>>> below.
>>> 
>>> Thanks
>>> 
>>> Krys
>
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-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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