At 03:24 AM 18/06/2003, muehleisen wrote: >Dear Dr. Smyth, > >if I use the function "normalizeForPrintorder" like the following > >Af.slide.25 <- normalizeForPrintorder (RG.slides.25.28.29.30.flagged, >layout=list(ngrid.r=12, ngrid.c=4, nspot.r=21, nspot.c=21), plot=FALSE, >method="loess", span=0.4), I get the error message Error in .local(...) : >formal argument "R" matched by multiple actual arguments. Even I split the >RG list object (containing slides 25, 28, 29 and 30) to a R and a G vector >(each containing only slide 25) like the following > Af.slide.25 <- >normalizeForPrintorder (Rraw.slide.25, Graw.slide.25, >layout=list(ngrid.r=12, ngrid.c=4, nspot.r=21, nspot.c=21)) I got the same >error message. This error arose because I tried to get clever with object orientated programming in R, and it doesn't work as I expected. I have revised the functions by going back to an older but simpler style and they should all work again. >However, if I use the function "plotPrintorder" like > >plotPrintorder(Rraw.slide.25, Graw.slide.25, layout=list(ngrid.r=12, >ngrid.c=4, nspot.r=21, nspot.c=21), method="loess", >separate.channels=FALSE, span=0.4), I surprisingly get the plot. In >general, what span do you recommend for "normalizeForPrintorder" and >"normalizeWithinArrays"? The default values are what I would recommend. >Would you please send me an example for "normalizeForPrintorder"? The help document now has an example using data from the SMA package, see limma version 1.1.2. Best wishes Gordon >Thank you in advance!!! > >Sincerely, > >Thomas W. Muehleisen > > >Max Planck Institute for Brain Research >Deutschordenstrasse 46 >D-60528 Frankfurt/Main