[BioC] Re: NA's

[Robert Gentleman]

And please, let's move these to bioconductor, they are of general
interest rather than specific to the management of the project


On Wed, Mar 27, 2002 at 12:22:39PM -0800, Anthony Rossini wrote:
> Raf - it might be worth documenting your opinions on the matter, to start thinking of how the various approaches compare under different situations.  Or is there already a paper on the topic?  (I'm sure in the substantive literature, but as to quality...?).
> 
> best,
> -tony
> 
> ---
> A.J. Rossini                            Rsrch Asst Professor of Biostatistics
> rossini@u.washington.edu                http://software.biostat.washington.edu/
> Biostatistics/Univ. of Washington       206-543-1044 (3286=fax) (Thursdays)
> HIV Vaccine Trials Network/FHCRC        206-667-7025 (4812=fax) (M/Tu/W)
> (Friday location is generally unknown).
> 
> 
> On Wed, 27 Mar 2002, Rafael A. Irizarry wrote:
> 
> > i have many.. but too complicated for email. call me if you want. a simple
> > one (that i dont like much) is to use a hybrid log. checkout hlog in
> > madman/Rpacks/affy/R/hlog.R
> > 
> > On Wed, 27 Mar 2002, 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
> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > 
> > > 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B28
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