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

[Matt Ritchie]

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