[BioC] Re: NA's

[Laurent Gautier]

The use of something like the 'na.action' mentioned before now would let us
(or others) plug-in easily their way to treat the NA's.. 


what  about  something  like

  log.na  <- function(x, na.action=<eventually put a default action here>) {
    x <- na.action(x)
    log(x)                                                                                      
  }



note: the handling of negative intensity values could be of general interest...
would it make sense to have the collection of function suggested by Yee and
Sandrine in a specific package (or in Biobase) ?



L.
                                                                                                                         
                                                                                                                         
                                                                                                                         
                                                                                                                         
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Laurent Gautier                  CBS, Building 208, DTU
PhD. Student                     D-2800 Lyngby,Denmark
tel: +45 45 25 24 85             http://www.cbs.dtu.dk/laurent
~                                                                              


On Wed, Mar 27, 2002 at 12:02:53PM -0800, Yee Hwa Yang wrote:
> Hi All,
> 
> Sandrine and I are working on some cDNA data where we find there are lot's
> of negative values which in turn produce NA's after log transform.  These
> negative values arise because foreground intensities are smaller than the
> background intensities (from image analysis output).
> 
> For sma, we had created a series of functions (log.na, sum.na, mean.na,
> ...) to handle NA values. For example, we have
> 
>  log.na
> function (x, ...)
> {
>     log(ifelse(x > 0, x, NA), ...)
> }
> 
> Does anyone have any suggestions about dealing with NA issues in
> general for cDNA array data?
> 
> Thank you,
> Jean & Sandrine
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>   Jean Yee Hwa Yang
>   Department of Statistics, 367 Evans Hall
>   University of California, Berkeley, CA 94720
>   Email:  yeehwa@stat.berkeley.edu
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> _______________________________________________
> Biocore mailing list
> Biocore@stat.math.ethz.ch
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other email: lgautier@altern.org
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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			D-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent


----- End forwarded message -----

-- 
--------------------------------------------------------------
other email: lgautier@altern.org
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			D-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent