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@fhcrc.org> > To: "anthony.ferrari@ensimag.imag.fr" <ferraria@ensisun.imag.fr> > Subject: Re: [R] marrayNorm package > > Your question should be directed to the bioconductor help list: > > bioconductor@stat.math.ethz.ch > > > On Fri, 2 Apr 2004, anthony.ferrari@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@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 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >