[BioC] Lumi: LumiT vst transform error

[Pan Du]

Hi Sarah 

The information you provided is too limited, I cannot answer your question.
At least, you need to provide sessionInfo() and the information of lumi.B.
You can also send me a subset of lumi.B, for example,
  test = lumi.B[1:5000,]
  save(test, file='test.Rdata')
and send me 'test.Rdata' file.


Pan 



On 2/26/11 5:00 AM, "bioconductor-request at r-project.org"
<bioconductor-request at r-project.org> wrote:

> Date: Fri, 25 Feb 2011 11:39:12 +0000
> From: Sarah Allen <sa413 at cam.ac.uk>
> To: bioconductor at r-project.org
> Subject: [BioC] Lumi: LumiT vst transform error
> Message-ID: <0C717235-749C-4C91-85F3-9F19AED64DBA at cam.ac.uk>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
> 
> Hello, I am having a problem performing vst normalisation on my data.
> I get the following error message that I can't make head or tail of:
> 
>> lumi.T <- lumiT(lumi.B)
> Perform vst transformation ...
> 2011-02-25 11:07:29 , processing array  1
> Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
>    0 (non-NA) cases
> 
> I have searched the archives and found that people have asked the same
> question before and the advice has been to update their Bioconductor
> package. All my packages are up to date, I have made sure that all my
> values are positive using lumiB "forcePositive", my boxplots all look
> fine (there is nothing intrinsically weird about my data) ... I am
> stumped.
> 
> Can anyone help?
> 
> Many thanks, Sarah Allen