Dear members of the Bioconductor mail-list dear maintainers of the limma and marray packages I wonder if there is proper handling of the Agilent 44K arrays is implemented in marray. Meanwhile I'm analyzing my human 44K in limma, and everything works fine with a great help of the list and almost perfect userguide (I'm rather biologist, than bioinformatician). Than the question appears to try "globalMAD" normalization from marray. Excited with limma userguide words about easy conversion of the RGlist data to marrayRaw object. I started in LIMMA like this: >RG.raw <- read.maimages(files = targets$fileName, path = loadPath, source = "agilent", quote="") ... >dim(RG.raw) [1] 43931 29 >RG.raw$genes$Status <- controlStatus(spottypes, RG.raw) Matching patterns for: ControlType Found 43931 Probe Found 314 Negative Found 1942 Positive Setting attributes: values Color SEEMS FINE so far > data.raw <- as(RG.raw, "marrayRaw") > summary(data.raw) ... A) Layout of spots on the array: Array layout: Object of class marrayLayout. Total number of spots: Dimensions of grid matrix: rows by cols Dimensions of spot matrices: rows by cols Currently working with a subset of spots. Control spots: There are 3 types of controls : Negative Positive Probe 314 1942 41675 Notes on layout: ... > data.norm <- maNorm(data.raw,norm="loess",echo=TRUE) Normalization method: loess. Normalizing array 1. Error in if is.int(totalPlate)) { : argument is of length zero OOPS :) Petty, It seems that marrayLayout is wrong. Than I thought that import of the data is implemented better than the conversion in marray I tried in frame of MARRAY: > data.marray.raw <- read.Agilent(fnames=targets$fileName, quote="") > summary(data.marray.raw) ... A) Layout of spots on the array: Array layout: Object of class marrayLayout. Total number of spots: 12900 Dimensions of grid matrix: 1 rows by 1 cols Dimensions of spot matrices: 30 rows by 430 cols Currently working with a subset of 12797spots. Control spots: There are 3 types of controls : Negative Positive probes 47 311 5837 Notes on layout: ONCE again, something wrong with layout However maNorm() is working w/o reported mistakes, but I wonder what is it normalising... Does anybody have any clue how to deal with Agilent 44K within marray? I searched for the archive, and did find the rare discussions on this, but didn't find the answer. I wonder as well if this problem is fixed in the developing version of the MARRAY And finaly, as advised below is > sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: convert marray vsn Biobase gplots gdata gtools limma "1.4.0" "1.8.0" "1.8.0" "1.8.0" "2.3.0" "2.1.2" "2.2.3" "2.4.13" > Waiting for advices... -- -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064