[BioC] Missing values with COPA

[James W. MacDonald]

Hi Francesca,

I'm no missing data expert, but heuristically, I think the 
pamr.knnimpute() function makes sense. However, I would look closely at 
your results to make sure you aren't getting too many significant genes 
with imputed values, where 'too many' is a term meant to let me say 
something without really saying anything ;-D

Seriously, though, I wouldn't imagine doing the knnimpute would cause a 
bunch of your genes to suddenly look significant for copa when they 
wouldn't if you didn't need to impute. I would just recommend the sanity 
check of looking at the results and making sure that the imputation 
isn't doing something unexpected.

Best,

Jim

Francesca Guana wrote:
> Dear James,
> 
> now the package COPA works well, if the data don't have missing values. Is
> that right?
> My original data have missing values, so I run pamr.knnimpute to impute
> missing expression values. Do you think this is a good procedure? Otherwise
> do you have any suggestion?
> 
> Best regards
> Francesca Guana
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.