[BioC] Lumi: LumiT vst transform error

[Pan Du]

Hi Sarah

After checking your data, I found the data has already log2 transformed. The
VST transformation should be on the raw scale. So please convert your data
to raw scale first, then you can apply vst.
 exprs(x.lumi) <- 2^(exprs(x.lumi))

I will also add checking code in the lumi package to give warning message in
the cases like yours. Tell me if the problem still exists.


Pan


On 2/27/11 8:04 AM, "Sarah Allen" <sa413 at cam.ac.uk> wrote:

> Hello, thanks for your reply. I have attached the session info and the
> file of lumiB like you said. Let me know if you need anything else.
> Thank you very much for your time. Sarah
> 
> 
>> sessionInfo()
>> 
> 
> On 26 Feb 2011, at 15:35, Pan Du wrote:
> 
>> 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
>>