[BioC] lumiT VST error

[Pan Du]

Hi Will,

Can you provide the sessionInfo()? Like the version of lumi you are using. I
guess you are using the old version of lumi. Thanks!

Pan


On 7/12/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 1
> Date: Wed, 11 Jul 2007 11:25:53 +0100
> From: William Mifsud <wm237 at cam.ac.uk>
> Subject: [BioC] lumiT VST error
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <C04F805E-E42D-4091-BDD2-F707B4B1EBF4 at cam.ac.uk>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> 
> Dear Bioconductor,
> 
> I have a problem running vst in lumi, where I'm getting the following
> error:
> 
> "
>> mydata.lumi.B = lumiB(mydata.lumi, method='forcePositive')
>> mydata.lumi.B.T = lumiT(mydata.lumi.B)
> 2007-07-10 12:29:57 , processing array  1
> 2007-07-10 12:29:58 , processing array  2
> 2007-07-10 12:29:59 , processing array  3
> 2007-07-10 12:29:59 , processing array  4
> 2007-07-10 12:29:59 , processing array  5
> Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
>          0 (non-NA) cases
> "
> 
> When I change the transformation method in lumiT to 'log2', or to
> 'cubicRoot', I don't get any error message.  I have got this
> behaviour on both Mac OS X and Windows XP platforms.
> 
> Thanks,
> 
> Will
> -- 
> 
> William Mifsud
> Wellcome Trust/Cancer Research UK Gurdon Institute
> Tennis Court Road
> Cambridge
> CB2 1QN