[BioC] Gene filtering

[James W. MacDonald]

Heike Pospisil wrote:
> Hello Adaikalavan
> 
>> I think justRMA() uses nearly all the memory you have access to, so it
>> it only able to handle small computations afterwards. What I would
>> suggest is try saving the exprSet and exit. Then start from a fresh R
>> session and do your analysis from that. See below.
>>  
>>
> 
> Thanks for your suggestion. Saving and loading the exprSet work and 
> help. But, unfortunately, my filter function do not work.
> 
> ff1<-ttest(data,.001,na.rm=TRUE)
> ff2<-filterfun(ff1)
> wh2<-genefilter(exprs(data), ff2)
> 
> No idea :-(
> 
> Best wishes.
> Heike
> 
I think you are setting up ff1 incorrectly. As an example, let's say 
that your exprSet contains 10 samples, the first 5 are e.g., 
experimental, and the second 5 are control. Then you would set up ff1 
like this:

ff1 <- ttest(5, 0.001, na.rm = TRUE)

-or-

cl <- c(rep(1,5), rep(2,5))
ff1 <- ttest(cl, 0.001, na.rm = TRUE)

The second method can be used if the samples are not contiguous (e.g., 
they are ordered exp, cont, exp, cont, etc).

cl <- c(rep(c(1,2), 5)
ff1 <- ttest(cl, 0.001, na.rm = TRUE)

HTH,

Jim



-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109