FW: [BioC] Re: [R] marrayNorm package (fwd)

[Jean Yee Hwa Yang]

Hi Anthony,

See help(maSub)

maSub isn't a vector representing "good spot".  Instead, its is there to
indicating which spots are currently being considered in the matrix maGf,
maRf, maRb, maGb etc  It is used to enable correct calculation of the
print-tip and plate information.  E.g

If the original matrix is x = 100 by 5 and you applied a subset of 
x[1:10,]
then maSub will be a logical vector of length 100 with the frist 10 values
equal to TRUE and the rest equal to FALSE.

If you want to filter the data file before ploting.  You simply use the
subset notation. 
i.e.
maPlot(swirl[1:100,])

Cheers

Jean

> ---------- Forwarded message ----------
> Date: Fri, 2 Apr 2004 08:38:45 -0800 (PST)
> From: Douglas Grove <dgrove at fhcrc.org>
> To: "anthony.ferrari at ensimag.imag.fr" <ferraria at ensisun.imag.fr>
> Subject: Re: [R] marrayNorm package
> 
> Your question should be directed to the bioconductor help list:
> 
> bioconductor at stat.math.ethz.ch
> 
> 
> On Fri, 2 Apr 2004, anthony.ferrari at ensimag.imag.fr wrote:
> 
> >
> > Hello,
> > I'm a french student working on cDNA microarrays.
> > I decided to use the bioconductor packages and I have a problem with
> > normalization functions.
> >
> > As everybody who manipulates microarray data know, there are some spots
> > on the slide which are to be removed. In the marrayLayout there is a slot
> > "maSub" (logical vector) where one can define the good spots.
> > Besides, when you print the features of your slide there is a line :
> >
> > "Currently working with a subset of 18482 spots"
> >
> > so it seems to be good.
> > BUT the problem is that the functions of marrayNorm package don't seem to
> > take the subset into account even when you fill the field 'subset' with
> > the 'maSub' vector.
> >
> > It seems to be the same with for instance the 'maPlot' function. It plots
> > all the spots of the array without taking the 'maSub' vector into account.
> >
> >
> > Anyone who can help me ?
> > I need help !!
> >
> > thanks
> >
> > Best regards,
> > Anthony Ferrari
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> >
> 
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