[BioC] Question about R and expresso()

[Laurent Gautier]

On Mon, Jun 16, 2003 at 03:50:59PM +0000, Daniel ~ wrote:
> 
> Hi,
> 
> We tried expresso() in R, but with bad luck.

Some people associate luck good or bad with numbers...
Could we know what are the version numbers for both R and the
package 'affy' ?



> 
> >eset <- expresso(data, bgcorrect.method="mas", normalize.method="qspline", 
> >pmcorrect.method="subtractmm", summary.method="playerout")
> background correction: mas
> normalization: qspline
> PM/MM correction : subtractmm
> expression values: playerout
> background correcting...done.
> normalizing...[1] "samples= 100 k= 5 first= 0"
> Error in rep(data, t1) : invalid number of copies in "rep"
> In addition: Warning message:
> 'k' found is non-sense. using default in: 
> normalize.qspline(t(intensity(abatch)), ...)
> >
> 
> 
> In R we want to imitate the .CHP file we get from an .CEL file in
> Affymetrix Microarray Suite. Is there anyone that know how to tweek
> the parameters in expresso() to reach that result?

There is no parameter I know of that would do that.
However, other functions (eventually added by snippets of R code you made)
should let you have what you want.


Hopin' it helps,


L.