[BioC] Romer warning serious? and nrot=9999?

[Gordon K Smyth]

Dear Loren,

> Date: Wed, 05 May 2010 09:28:45 -0700
> From: Loren Engrav <engrav at u.washington.edu>
> To: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Romer warning serious? and nrot=9999?
>
> So ran romer with
> romer(iset, y, design, contrast, array.weights=NULL, block=NULL,
> correlation, floor=FALSE, nrot=9999)
>
> Finished with no errors but I see
>
> Warning
> In romer (iset, y, design, :
> Estimation of var.prior failed ­ set to default value
>
> romer2 finished with same message

Unlikely to be a problem.  It does suggest though that your dataset is 
relatively small or a bit unusual.

> Am I in trouble?
> Or can I ignore this?
>
> Also
> Did nrot=9999, is 9999 really necessary? Or is 1000 good enough?

The smallest possible p-value is 1/(nrot+1).  So nrot=999 (or 1000) means 
the smallest possible raw p-value is 0.001.  This may not be very 
convincing if you have tens of thousands of sets.  Personally, I use 
nrot=9999 or greater.

Best wishes
Gordon