Entering edit mode
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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> > > Biocore@stat.math.ethz.ch
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> > >
> >
> > _______________________________________________
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> >
>
>
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