Dear Mike, At 09:05 PM 13/06/2003, michael watson (IAH-C) wrote: >Hi Gordon > >I have finally found some time to try out limma and have come across some >problems. > >I am using the following: > >Package: limma >Version: 1.0.3 >Date: 2003/05/04 >Title: Linear Models for Microarray Data >Author: Gordon Smyth <smyth@wehi.edu.au> >Maintainer: Gordon Smyth <smyth@wehi.edu.au> >Depends: methods, modreg, MASS, splines, nls, nlme, R (>= 1.6.1) >Description: Data analysis, linear models and differential expression for >spotted and oligonucleotide microarrays. >License: GPL version 2 or newer >URL: http://bioinf.wehi.edu.au/limma/ > > >I am having trouble calculating MA values. Having read in some genepix >data using > >RG <- read.maimages(..., "genepix") > >I then got the following: > >MA2 <- normalizeWithinArrays(RG,lout,method="loess") >Error in residuals(loess(y ~ x, weights = w, span = 0.75 * span, na.action >= na.exclude, : > couldn't find function "loess" Sorry, my mistake. The 'loess' function is part of the 'modreg' package which you don't have loaded. You just need to type library(modreg) at the R prompt and then the command that you give above will work fine. I thought that I had arranged for 'modreg' to be loaded for you automatically if needed, but apparently not. Note that this particular problem will disappear if you upgrade to R 1.7.0 or later because 'modreg' is now loaded by default as part of R. >also, the following commands worked but produced THE SAME MA values: > >MA <- normalizeWithinArrays(RG,lout,method="none") >MA1 <- normalizeWithinArrays(RG,lout,method="lowess") > >I suspected that method was defaulting to some default method so I tried: > >MA <- normalizeWithinArrays(RG,lout,method="crap") > >and again got the same MA values. You are quite right, if the method requested is not even a partial match for any of the possibilities, then no normalization is done. > Shouldn't there be a warning when the method is not recognised?? Yes, perhaps there should be. > Also, the documentation says method="loess" should work, but i just get > the above error message > >Otherwise this was looking like quite a nice package... :-D Thanks for your comments. >Thanks >Mick Note that 'limma' is up to version 1.1.0 now. Gordon ---------------------------------------------------------------------- ----------------- Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia Tel: (03) 9345 2326, Fax (03) 9347 0852, Email: smyth@wehi.edu.au, www: http://www.statsci.org

At 11:32 PM 20/06/2003, michael watson (IAH-C) wrote: >Hi Gordon > >I'm still playing with limma and just came across another oddity you may >or may not be aware of! > >In the help for imageplot(), your example is this: > >M <- rnorm(8*4*16*16) >imageplot(M,layout=list(ngrid.r=8,ngrid.c=4,nspot.r=16,nspot.c=16)) > >Here we see that the array consists of 8 rows of sub-grids and 4 columns. > >However, if I execute this command, i get a plot with 4 rows of subgrids >and 8 columns...? I deliberately chose to plot arrays on their side, i.e., the "top" of the array is on the left of the screen. That is why the help document says that the first spot on the array is on the bottom left of the plot. I choose to do this because most computer screens are wider than high. >Also, is there way of generating the matrix of data easily from say a >GenePix file? >I find this difficult as GenePix just has a single co-ordinate for a >sub-grid called >"Block" and there is nothing in the actual file to say how many rows and >columns there are. Do you mean generate the layout parameters? If you have a GenePix allocation list (gal) file in your working directory with extension ".gal", then you can type gal <- readGAL() layout <- getLayout(gal) to extract the layout parameters. >However, even with user input, it would be good to be able to convert from >a list to a matrix > >Thanks >Mick Gordon