[BioC] Biobase or affy package makes update() not work

Dick Beyer dbeyer at u.washington.edu
Wed May 26 18:00:20 CEST 2004

In previous versions of R and bioconductor, I was able to make an initial call to lme(), then use update() inside a loop.  I can still do that if I don't load any bioconductor packages.

For example,

  ge     <- xx[1,]
  age    <- c(0,0,1,1,0,0,1,1,0,0,1,1)
  gen    <- c(0,1,0,1,0,1,0,1,0,1,0,1)
  fdr    <- c(0,0,0,0,1,1,1,1,3,3,3,3)
  dat    <- data.frame(age, gen, fdr, ge)
  ge.lme <- lme(fixed=ge~age+gen+age*gen, data=dat, random=~ 1| fdr)

works fine.  If I then load affy and try update() again, I get an error:

Error in update(ge.lme) : No direct or inherited method for function "update" for this call

I am using windows 2000 and the following packages:

base 1.9.0 
utils 1.9.0 
graphics 1.9.0 
stats 1.9.0 
methods 1.9.0 
nlme 3.1-48 
Biobase 1.4.14 
affy 1.4.30 
xtable 1.2-1 

Would anyone have an idea of what is happening?

Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099

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