[BioC] question about Limma

? ? chenhuan7809 at msn.com
Fri Jul 22 12:34:48 CEST 2005

Dear Sir
    I am a novice to limma. I meet some questions and can't solve these by 
myself. So please give me a hand.
    firstly, I wonder could I use two wt.fun to filter bad spot, for 
myfun1 <- function(x, threshold=50) {
    + okred <- abs(x[,"F635 Median"]-x[,"F635 Mean"]) < threshold
    + okgreen <- abs(x[,"F532 Median"]-x[,"F532 Mean"]) < threshold
    + as.numeric(okgreen & okred)
myfun2 <- function(x) as.numeric(x$Flags > -99)
I think "myfun1" can help me to filter outliers and "myfun2" can help to 
filter bad spots according to Genepix output file(.gpr file). Could I 
combind two filter ways to filter spots, and how?
    Secondly, question about "duplicateCorrelation", there is a example in 
your limma usersguide to solve all genes (ESTs and controls) are printed 
more than once on the array, in my microarray, every gene have 
duplication,the command is "cor <- 
duplicateCorrelation(MA,design,ndups=2)", but when I do some technical 
replication, how can I use this function? (when it comes to technical 
replication, ndups will equal to 1,how to compute correlation within array 
duplication? And I isolate RNA from bacterial not animal bodys, how to say 
biological replication?).
    Finally, how to extract information from the eBayes function, I mean 
could I get $coef,$lods,$genes,etc simultaneously, as .gal file input 
Thanks your help.
Best regards

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