[BioC] prepare data matrix for siggenes

[Maciej Jończyk]

Hi Joseph,

From: joseph <jdsandjd at ...>
Subject: Re: prepare data matrix for siggenes
Newsgroups: gmane.science.biology.informatics.conductor
Date: 2011-04-04 19:28:35 GMT (55 minutes ago)

> Hi Holger
> I got an Warning message when I used the data:
>
>> sam.out = sam(sumis, cl, rand = 123, gene.names = sumis.names,
var.equal =
>>TRUE)
> We're doing 70 complete permutations
> Warning message:
> There are 2 variables with zero variance. These variables are removed,
> and their d-values are set to NA.
>
> how serious is this warning, and how can I identify the 2 variables
with zero
> variance?

It's variables for which all values are equal, so without variability.
Consequently variance is equal to 0 for these variables.

I think you should check your data, no variability is rather strange
and may be an artefact.

Hope this helps,


> thanks
> Joseph


Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



___________________________________
NOCC, http://nocc.sourceforge.net




-- 
This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com