Hi,

I'm using the marray package to analyse my 2-color cDNA array data,  
and I'm trying to sort out how to tell the various functions which  
spots to use.  I understand how to set the maSub vector in the layout  
object, and my understanding is that the normalization functions will  
then use this vector to know which spots to include in the  
normalization procedures so long as subset=TRUE when I call a given  
normalization function.  But how do I flag spots within specific  
arrays such that those spots will not be used in the normalization or  
in the limma methods?  For example, here is some code a friend of  
mine was using to flag spots for normalization methods using the  
limma function read.maimages():

#this function flags out bad spots defined as saturated, too small or  
large, absent or manually flagged as bad.
filters <- function(x) {			
      okred <- x[,"F635 Mean"] < 65534	
      okgreen <- x[,"F532 Mean"] < 65534
      fat <- x[,"Dia."] > 50
      skinny <- x[,"Dia."] < 150
      present <- x[,"Normalize"] < 1
      good <- x[,"Flags"] > -50.5
      as.numeric(okred & okgreen & fat & skinny & present & good)
}

#read in data and gal file
RG = read.maimages(targets$FileName, source="genepix",  
wt.fun=filters, other.columns=c("F635 SD", "B635 SD", "F532 SD",  
"B532 SD", "F Pixels", "B Pixels", "B532 Mean","B635 Mean"))

So now, because of the wt.fun parameter, those spots are considered  
(or not) according to the filter function.  What would be the  
corresponding way to do this using marray?  I'm assuming I must set  
the name.W parameter when I call read.marrayRaw() to point to a  
vector indicating the weights of each spot.  If so, I can handle  
this, but how do I ensure that the normalization methods will use  
this vector?  If the name.W parameter is set in the marrayRaw object,  
will maNorm() know to use it by default?  Or must I tell it that it  
is set in some way?  What about lmFit()?

Thanks,

Jay

--
Jay H. Konieczka
Ph.D. Student, Antin Lab
Molecular & Cellular Biology
University of Arizona

Phone:  1.520.591.3446

1656 E. Mabel, MRB 317
Tucson, AZ 85724 USA
_____________________



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