Hi everyone! I was hoping that someone here might have some insight on this problem: I do normalization between arrays. For this I have written a little program which creates an R/Bioconductor program which does this for me. It usually works fine but now I have a set of GPR files where it fails. This is how it goes: First it loads the libraries: library(marray) library(convert) Then it loads the GPR files: files <- c("gpr_file__0", "gpr_file__1", "gpr_file__2") Rf_label <- "F633 Median" Rb_label <- "B633 Median" Gf_label <- "F543 Median" Gb_label <- "B543 Median" g <- read.GenePix(files, name.Gf = Gf_label, name.Gb = Gb_label, name.Rf = Rf_label, name.Rb = Rb_label) A print tip-loess normalization for every slide: gn <- maNorm(g, norm="p") Then comes the normalization between arrays. I use the "normalizeBetweenArrays" command here. I basically just copied the commands from the book "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" on page 65: gn at maW <- matrix(0,0,0) gn.MA <- as(gn, "MAList") g.nbta <- normalizeBetweenArraysgn.MA, method="quantile") This has always worked. But in this case I get the following message after the second command: > gn.MA <- as(gn, "MAList") Error in "$<-.data.frame"(`*tmp*`, "Sub", value = c(TRUE, TRUE, TRUE, : replacement has 7200 rows, data has 6912 Execution halted This, at first glance rather puzzling message, seems to have something to do with the "maSub" Slot of the GPR files. According to the docs, this field is "indicating which spots are currently being considered." It is of type boolean and 6912 values are set to TRUE and the others are FALSE. Huh? Why aren't all spots being considered? If I insert maSub(gn)<-TRUE before the command that fails, the normalization seems to work just fine. However, I am wondering where the values from maSub come from and if it is a good idea to just override them. Does anybody know this? Thanks in advance for hints, Michael. -- ----------------------------------------------------------- Dipl.-Inform. Michael Nuhn Bioinformatik Zentrum f?r Nanostrukturtechnologie und Molekularbiologische Technologie +49 (0)631 - 205 4334 nuhn at rhrk.uni-kl.de http://nbc3.biologie.uni-kl.de/

Hello Gordon! > First of all, an incidental but important point. The subject of your email says > "normalizeBetweenArrays gives an error" but this is not true. Your error came when you tried to > convert an marrayNorm object into an MAList object. You never got to the point of using > normalizeBetweenArrays. You would have a better chance of getting help from the right people if > your email subject said "converting marrayNorm to MAList gives an error" or similar. Yeah, that was not very smart. > The purpose of the maSub slot is to record incomplete gpr files. The fact that maSub has length > 7000 with 6912 TRUE values means that the number of print-tip groups on your arrays implies 7000 > spots but actually 88 of these spots are omitted from your gpr files, probably because they are > "empty" or "blank" spots. Since you are in a Bioinformatics group, you're probably a computer > savvy person, so you can probably confirm easily that your gpr files contain only 6912 data rows. Ah, ok, thanks for that. I will ask the biologist who designed the array about the empty spots but I guess thats the reason for my problem. And as the computer savvy person I am, I have checked the GPR file and there are indeed only 6912 data rows. > In your case, you have already completed print-tip loess normalization on your data object. So > you no longer have any need to keep track of which spots are from which print-tip group. So you > could simply set maSub(gn) <- TRUE without any problems. Done. Thanks for your help Gordon and greetings from Germany, Michael. -- ----------------------------------------------------------- Dipl.-Inform. Michael Nuhn Bioinformatik Zentrum f?r Nanostrukturtechnologie und Molekularbiologische Technologie +49 (0)631 - 205 4334 nuhn at rhrk.uni-kl.de http://nbc3.biologie.uni-kl.de/