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

[Loren Engrav]

Thank you

Small data set? Yes, my data set is small, 1842 genes of interest at week1 2
3 12 or 20 between Duroc and Yorkshire breeds after filters

And the warning occurs only for week1 where the differential is the smallest
of all 5 time points with only a handful of differentially expressed genes

9999? I can run 9999 but the variance in this complex biological system is
large so I probably cannot claim .0001 precision, and we are "screening" at
this point

but if something "interesting" appears I will check that out with 9999

Thank you




> From: Gordon K Smyth <smyth at wehi.EDU.AU>
> Date: Fri, 7 May 2010 10:27:36 +1000 (AUS Eastern Standard Time)
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: rbioc <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Romer warning serious? and nrot=9999?
> 
> 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